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The adsorption capacity was calculated using molecular simulation. When the adsorbent is MOF or COF, it is often mentioned in the literature that the molecular structure of the adsorbent needs to carry charge data. However, I don't know exactly how the charge affects the adsorption capacity, and how much?
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Surface charge will either attract or repel the adsorbate. So surface charge definately plays an important role in adsorption. When you do your adsorption studies for an adsorbent, it will be based on the surface charge of teh adsorbent. However, if you place the adsorbent in a different environment or solution thati changes its surface charge, you need to repeat thea dsorption studies for it in this new environment.
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Every time I start loading a lammps dump file of more than 4GB in windows, VMD crashes. Are there any certain modifications I need to make?
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Hey There, The most probable reason is that your machine memory (RAM) < what is required by VMD for visualizing the dump file. VMD uses 12 bytes of memory /atom /frame, so you can calculate the memory required by the formula 12*Number of atoms*Number of frames.
Solutions:
1. Load a subset of your dump file, either by limiting the start/end frame indices or by setting a frame stride greater than 1 when loading the trajectory.
2. Expand your workstation specs.
I hope this helps.
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Hi,
I am a new user of ORCA. My initial calculations were successful but at this moment I am facing a problem to run a new calculation on my laptop. However, I can run calculation with the same input file on my older laptop.
Here is an example of my input file for the calculation on nitric oxide:
!RKS BP86 RI SV(P) SV/J TightSCF Opt
*xyz 0 2
N 0 0 0
O 0 0 1.2
*
Here is the error message mentioned at the bottom of the .out file:
ERROR : GSTEP Program returns an error
cannot continue with the optimization
COMMAND : orca_gstep NO.ginp.tmp
RETURN CODE : -1
I would appreciate your help.
Best regards,
Subrata
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This is due to the difference between the number of cores in the input and sbatch files.
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Dear all,
I have been confused about the use of restraints in the molecular simulation. As far as I understand, the restraints are added in energy minimization so that only the solvent will optimize and it will orient correctly around our protein. The equilibration is considered the relaxation towards equilibrium of the system, but as the large motion of the protein before sampling is unwanted, the restraints are added again.
Yet, I by chance heard from a senior research that for dt=1fs nvt equilibration, we should not add constraints. (only added for 2fs)
I wonder whether 'constraint' here means 'restraint' or not. If it's restraint, then why should we removed it in case of shorter time steps?
Or maybe I have mistaken the definition/ purpose of the processes?
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In MD simulations, atoms of the macromolecules and of the surrounding solvent undergo a relaxation that usually lasts for tens or hundreds of picoseconds before the system reaches a stationary state. This stage of the MD simulation is called equilibration stage.
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I am working of oxidative stress and found out one target protein form network pharmacology approach. We tried the molecular docking studies with some triazol derivatives. This gave us good result. Now we are planning to do wet work with this system but meanwhile i would like to so some simulation studies on the same. If any body is interested in collaboration pl mail me on
Dr. Manisha Modak
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Good Idea!!
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I am trying to run a QM/MM in Amber on a protein-ligand system. I have looked for tutorials but they don't explain a few things such as how to heat your system and equilibrate it before MD.
Then there are errors in output files. I have run the questions in the list and applied the changes, but the errors still remain. I would appreciate if someone could share their experience on running these for protein-ligand systems.
Thank you.
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Dear Ayesha,
This tutorial (https://ambermd.org/tutorials/advanced/tutorial2/section3.htm) explains how you can prepare your system, submit it to MD simulations and run QM/MM calculations. Your system is heated during the "heating" step from the classic MD topic.
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I have a 20a x 17a x 20a simulation box filled with bcc tungsten atoms. What lammps command can I write to make 20a x 2.5a x 20a at the bottom of the box "immobile"?
The script below shows how my atoms were created:
# ---------- Create Atoms --------------------------
## define crystal structure and lattice constant a_0
## define direction vectors, i.e., set x=[100], y=[010], z=[001] and origin point.
variable a_0 equal 3.1648
lattice bcc 3.1648 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 &
origin 0.1 0.1 0.1
region box block 0 20 0 17 0 20 ## define box sizes along x, y, z (in the unit of a_0)
create_box 1 box ## create the simulation box, allowing a max of one specie
create_atoms 1 box ## create type-1 metal atoms in the box
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Dear Nitin,
Can you share the script where some of the atoms in a slice (group) can be made mobile. This is specifically an interdiffusion of two materials I.e. setting up bonding/Welding etc. Exact problem is to make one body thermostat and another body to heat up say via NVT.
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So, My question is what basis we choose the membrane proteins for docking and molecular simulations, because in PDB there are a lot of structures for membrane proteins Like GPCRs, Ionic linked receptors, and Enzyme-linked receptors.
Above mentioned I have some knowledge about the PDB structures for choosing based on the Resolution 1-3 b/w, this range is good crystal structure.
But, the problem is how nanoparticles interact with membrane proteins? So, what basis we choose the PDB structures for docking.
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What is your nanoparticles? You can use openmm to build several nanoparticles.
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I use VMD for analysis of NAMD molecular simulation.
I have gotten a RMSF plot using a scrip via VMD.
As it obvious, residue number 1399, attained maximum fluctuation in this plot.
Now I wanna know residue number 1399 belongs to which amino acid in my protein structure.
BTW: I have to use stride=80 because of large dcd file.
I have attached the RMSF script I used and also the RMSF plot.
Help me if you can
Thanks.
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1. Upload your PSF and DCD files into the VMD.
2. Click on Graphics and select Representations.
3. Type the keyword "resid 1399 and not water" in Selected Atoms
4. Press enter
5. In Coloring Method choose ColorID red in adjacent tab
6. In Drawing Method choose Licorice
7. Now you can see your selected residue number in VMD OpenGL Display
8. Now press 1 in your keyboard and click on that selected residue number
9. Now you can see the residue name of your selected residue number.
Hope you will get the information which you want to know.
Thanks
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Hello Everyone!
I am working on molecular simulations of nanoparticles and for that I have to use LAMMPS. I want to install LAMMPS on Linux and tried several tutorials but couldn't install it anyway. Currently I am watching and trying this tutorial "https://www.youtube.com/watch?v=FMjwSdPAT3k&t=243s" but doesn't get its some of codes as its not working on my side. Can anyone please give me some good tutorial of LAMMPS with complete guideline of its installation?
Your answers are highly appreciated
Regards & Thanks
Misbah
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Just type these codes one by one
$ sudo add-apt-repository ppa:gladky-anton/lammps $ sudo add-apt-repository ppa:openkim/latest $ sudo apt-get update
$ sudo apt-get install lammps-stable
$ lmp_stable -in in.lj
$ sudo apt-get install lammps-stable-doc
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Dear all,
I have started to study molecular simulation for weeks, and have studied the basic theory of molecular simulation from lectures and videos. I am currently trying to do some hands-on practices, but here comes the question.
I follow the tutorials, yet I don't know how to come up with the protocol of my target. I have been puzzled 'how to study my target' for a while. Also, how to be familiar with my target is another big problem.
Can anyone please give me some suggestions? Study route or any recommendations are appreciated.
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Dear Tini Chu
To properly get started you need a solid theoretical background of thermodynamics, statistical thermodynamics and molecular dynamics in general. Many good books have been written over the years, such as
Computer simulation of liquids (Allen)
Understanding molecular simulations (Frenkel)
Molecular modelling (Leach)
Thermodynamics and statistical mechanics (Greiner)
When you have the theoretical tools, you need the practical ones. This mainly means finding a software which is able to run simulations of your system of interest, depending also on the hardware available. GROMACS, CHARMM, LAMPS are common examples of MD software. You have to decide what to use and install it if not already available to you.
Next, and arguably most important step, is setting up your starting systems, which roughly reduces to choosing a force field. What system are you interested in? What molecules? What timescales? Is the force field implemented in the MD software you are using?
At this point you will be able to start running simulations about your system of interest.
There is no general answer to these questions. Some software is better than another in certain aspects, or supports a force field that you need while others don't. Similarly, some force fields work better for some properties/molecules/systems than others. Maybe you are looking to be fast, and therefore are looking to coarse grained or united atoms systems.
A 'must do' is looking in the given field and understand what has been done and what is the common procedure to do it. If you are interested into binding properties of some ligand, then read relevant literature about it, maybe something has already been done with your ligand of interest. What software are they using? What force field? What properties do they measure? Once you have an idea, install and get experience with that software. For example, for GROMACS do some of these tutorials (first one always plus other relevant to you)
I use GROMACS as an example because that's what I work with, but CHARMM, LAMPS etc are available and you will for sure find many tutorials online. Once you are familiar with the software, find some fundamental work in the literature that is achievable and try to reproduce it, so that you get experience with a system similar to yours and with the sampling procedures you also will need.
Hope this helps,
Nicola
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I want to simulate polymers. Could you recommend any software to build the molecules? I want to do simulations to evaluate new polymers that were generated in my laboratory, could you recommend key properties that I should measure? I want to do molecular dynamics with gromacs because it is the software that I know how to use, but would there be any better? Could you recommend any guide or tutorial. Only free access software.
I already tried Charmm-gui but it doesn't have the polymers I need to model.
Thanks for your help,
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It is not difficult to create a new polymer. For example, it can be done by means of Avogadro software. Note that, obtaining proper force field parameters is a challenging task in MD simulations. The structural optimization and determination of partial charges can be performed by DFT calculations. In order to do that you have to parameterize your polymer which needs to represent the correct interaction parameters in hydrophobic and hydrophilic content. Please, find below links for several papers which might be helpful for your case:
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There is some software or tool that allows me to create a molecular simulation in which the pressure in my system is increasing?
I am working with a pressure sensitive membrane protein and I would like to analyze its behavior in molecular dynamics
Thanks!
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Usually you will either use an NPT or NVT ensemble. NPT is constant pressure that you set in the input file so you won’t be able to change the pressure. NVT allows pressure to fluctuate, but you can’t control the pressure. I may be mistaken, but it seems to me that changing the pressure would require re-equilibration to prevent the system crashing, so I don’t think using restarts at different set pressures would work (I guess you could always try). I think the way to go would be to use separate simulations. I would be to launch multiple replicas of NPT simulation at different pressures (say 25 replicas each) and then use the aggregate data sets to do your analysis. This method lends itself well to Markov modeling and other collective variable analysis as well but requires a lot of computational resources. Perhaps someone else will have a better suggestion, good luck to you.
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Dear All,
I have problem with pressure (virial) calculation. My task is quite different than normal. In my case I have total forces Fk on particle k treated as the sum of all the forces from the other particles j in the system. I have that information from external program (e.g. CP2K), off course I have also atoms positions all k particles. My question is how can I calculate a virial component (pressure) with that?
Thank You!
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Hello All
I am trying to calculate the frequency of a transition state of the molecule, but everytime the running jobs stops after calculating the rotational constant in the output file and shows" Error termination request processed by link 9999."
  I would be very thankful if anyone could help me with the reason of this problem and what can be done?
I already tried increasing the SCF Maxcycle, but it still got struck at the same point mentioned above.
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Another way is to increase %mem. Please refer to an outstanding report about "How to solve the error message in Gaussian" as follow: https://docs.computecanada.ca/wiki/Gaussian_error_messages
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I am trying to optimize a hexa-coordinated Cu-complex with N2O(N=N=O) as one of the ligand. My input file parameters are define below. Can anyone help me how to solve the problem?
N.B:- When I optimize the same Cu-complex without N2O(N=N=O) i.e- a penta-coordinated Cu-complex, it ends with normal termination .
%mem=2500MB
%chk=cu_complex.chk
# opt=maxcycles=500 b3lyp/3-21g scrf=(solvent=dichloromethane)
geom=connectivity
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Total agreement with the good colleagues using keyword opt=cartesian and nosymm or symmetry=none. An outstanding summary about "How to solve the error message in Gaussian" as follow: https://docs.computecanada.ca/wiki/Gaussian_error_messages
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For spin isomers such as ortho-parahydrogen, is it possible to study the catalytic addition of their mutual conversion through molecular simulation technology?
As we know that hydrogen has two spin isomers, specifically, they are orthohydrogen and para hydrogen. Now there are some studies that use catalysts to convert it catalytically. With the popularization of first principles, many studies have used molecular simulation methods to study problems at the atomic level, but it is rare to see that this method is applied to parahydrogen conversion. Is this method not working? Or are there other reasons for this phenomenon?Is there a combination of machine learning and molecular simulation technology to quickly screen the most favorable catalyst?
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Dear Zheng Gao this is a very interesting technical question. Since we are working in synthetic inorganic chemistry I'm certainly not a proven expert in this field. However, I can suggest to you a few potentially useful literature references. For example, please have a look at the following articles:
Para-ortho hydrogen conversion: Solving a 90-year old mystery
and
Hydrogen Conversion in Nanocages
(see attached pdf file)
The first article is freely available as public full text on RG, and the second one has been published Open Access.
Good luck with your research work!
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I have done one NVT molecular simulation for liquid phase propanol and one vacuum simulation for gas phase propanol simulation. However, my calculated heat of vaporization did not match with the experimental value. My liquid phase enthalpy was 21.52 KJ/mol and gas phase enthalpy was 31.6 KJ/mol. So, I got the heat for vaporization is 12.5 KJ/mol whereas, the experimental value is 42.5 KJ/mol. I suspect that the potential energy for liquid phase has having some problem. But, I could not figure that out. My liquid phase potential energy is -13.16 KJ/mol and kinetic energy is 34.68 KJ/mol.
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First of all, you need an interaction potential that accounts for hydrogen bonding. There are simple Lennard-Jones- or Mie-type effective potentials that can be used, but these are usually optimized for the liquid phase, and therefore are not very good for the vapour phase. Which potential/force field did you use?
Second, you have to ensure that both phases have the same pressure. You need
NpT simulations for this, and then you have to set the pressure to the equilibrium vapour pressure.
If you do not know the vapour pressure for your propanol model, you can either use a simulation technique that involves fluctuations of the particle number (e.g., grand canonical Monte Carlo or Gibbbs ensemble Monte Carlo) or to obtain the chemical potentials (e.g., Widom's insertion method or thermodynamic integration) and vary the pressure until the chemical potentials of the liquid and the vapour become equal.
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Hii,
I want to know if it is a good choice to do model refinement with online server like 3D refine after model generation instead of Molecular dynamics?
I have run the molecule simulations up to 10ns for my structure also but when I was docking the ligand after simulations ithe interactions were totally different?
So, I decided to do the refinement with 3D refine and after docking ligand interactions are somewhat similiar so I want to know if it is okay to use web server for refinement.
Thanks!
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Mahbubul Himel Rajesh Pal Nancy might be referring to the fact that protein molecules can be minimised/refined using YASARA or Galaxy Refine servers before performing MD simulations. Also, YASARA (and many other minimisation servers) do employ MD simulations to achieve the minimised state of protein molecules. For example, YASARA performs MD simulations (in an implicit solvent and using YASARA2 ff) until the Fmax reaches 0.05 kJ/mol/atom.
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I have been trying to finish the polymer tutorial for MARTINI, I was able to reproduce the bonded distribution, and I was also able to get the density, end to end distance and gyration radius within 5%. But I am not able to reproduce the solvation free energy in case of PEG9 in a solution. According to the tutorial I should get 7kJ/mol, but I am getting a value of 150kJ/mol. 
md.mdp file:
integrator = sd
; start time and timestep in ps =
tinit = 0
dt = 0.01
nsteps = 2500000
cutoff-scheme = group
; We remove center of mass motion. In periodic boundary conditions, the center of mass motion is spurious; the periodic system is the same in all translational directions.
comm-mode = Linear
; number of steps for center of mass motion removal =
nstcomm = 10;5 ; ORIGINALLY 10
ns_type = grid ; USER ADDED NOT IN TUTORIAL
pbc = xyz ; USER ADDED NOT IN TUTORIAL
table-extension = 2
; Output frequency for energies to log file and energy file =
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 10000
nstenergy = 10000
nstcalcenergy = 10
nstxtcout = 10000
nstlist = 10;10 ;5 ; ORIGINALLY 10
rlist = 1.4
coulombtype = Shift
;rcoulomb_switch = 0.0
;rcoulomb = 1.2
;epsilon_r = 15
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2
tc-grps = System
tcoupl = v-rescale
tau_t = 1.0
ref_t = 300
; Pressure coupling =
Pcoupl = Parrinello-Rahman
tau_p = 12.0 ; PREVIOUSLY 4
compressibility = 3e-4
ref_p = 1.0
;--------------------
; Free energy parameters
free-energy = yes
sc-power = 1
sc-alpha = 0.5sc-r-power = 6
sc-r-power = 6
; Which intermediate state do we start with?
-------
init-lambda-state = sedstate
; What are the values of lambda at the intermediate states?
;-------
vdw-lambdas = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0
; This makes sure we print out the differences in Hamiltonians between all states, and not just the neighboring states
;--------
calc-lambda-neighbors = -1
; the frequency the free energy information is calculated. This
; frequency (every 0.2 ps) is pretty good for small molecule solvation.
;-------
nstdhdl = 10
; not required, but useful if you are doing any temperature reweighting. Without
; temperature reweighting, you don't need the total energy -- differences are enough
dhdl-print-energy = yes
couple-moltype = PEG
; we are changing both the vdw and the charge. In the initial state, both are on
couple-lambda0 = vdw
; in the final state, both are off.
couple-lambda1 = none
; we are keeping the intramolecular interactions ON in all the interactions from state 0 to state 8
couple-intramol = no
Please help, I have been stuck at this tutorial for far too long. 
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It means that you do not need to multiply the potential energies with an arbitrary factor.
You still can do HREMD, but depending on the method you should think about changing angles/Lennard-Jones parameters instead of dihedrals and electrostatics. In the MARTINI coarse-grained representation, most molecules do not have dihedrals and electrostatic interactions are mostly parameterized within the VdW interactions (with a few exceptions).
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I have a target and a small molecule which is interaction with the enzyme. How do you determine whether the small molecule is a substrate or an competitive inhibitor of the enzyme?
I feel so confused because the substrates and competitive inhibitors of an enzyme are usually structurally similar.
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I would say by the reaction it causes to the enzyme. Maybe by the kind of binding,but I am not sure how to figure it out. Maybe measure it by the substrate/product.
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I am currently performing coarse-grained MD simulations in LAMMPS using mW potential for water. I initialize the water model at 273K, equilibrate for 50ns followed by a quenching process from 273K to 200K at a rate of 0.5K/ns for a total of 146ns. At the end I observe what looks like a nucleated structure. But how can I be certain that homogeneous nucleation has indeed taken place?
Can a specific property be extracted from LAMMPS or any visualization technique be used to confirm that the structure has indeed nucleated?
Any insight is appreciated.
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Write a script to calculate the radial distribution function of your system along a predefined reaction coordinate between the interface and the buried atoms. Check the coordination number and the behavior of the RDF to get insights about nucleation.
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I want to calculate just the distance between two neighbouring monomers using Avogadro but since it doesn't allow to create long chains, I am in this dilemma. Kindly help !!
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The distance between the monomers, depending on the length of the chain, but on the state of the macromolecule
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I am trying to do a molecular simulation for a single molecule at box dimension 15 A * 15 A * 15 A. But every time I am getting an error saying "1 of the 64 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (0.4 nm) or the two-body cut-off distance (0.4 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck"
Can anyone share the input command line for this type of simulation?
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thanks for your important question
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I'm working with molecular simulation of systems composed of nonspherical particles and currently interested in calculating the first- and second-order perturbation coefficients and comparing the results with the spherical case. These coefficents are related to the high-temperature power series expansion steming from Zwanzig's perturbation theory. I've come across an article ( ) that relates the ratio of these coefficients with the low-density limit. In other words:
a2/a1 = 0.5
or, in a most general case:
a_i/a_i-1 = 1/i
where a_i represent the perturbation coefficients and i is an integer number greater than or equal to 2. Does anyone know where this "perturbation ratio" comes from?
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Hi, I'm trying to do a simulation of my docking results and i got this error
Fatal error:
The residues in the chain MET1--NI602 do not have a consistent type. The first
residue has type 'Protein', while residue KCX219 is of type 'Other'. Either
there is a mistake in your chain, or it includes nonstandard residue names
that have not yet been added to the residuetypes.dat file in the GROMACS
library directory. If there are other molecules such as ligands, they should
not have the same chain ID as the adjacent protein chain since it's a separate
molecule.
I have tried adding residue name to residuetypes.dat and also added the residue to the forcefield at the aminoacids.rtp file based on previous papers but i'm still getting the error. perhaps im doing it wrong. in the residuetypes.dat i put KCX Protein but i still get the error as 'Other'. Where should i change the residue type? or is it because i put the wrong residue type?
anyone know how to solve this?
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You can use openforcefield to add a residue to a forcefield:
If you want to perfomed a protein-ligand complex simulation follow GROMACS tutorial:
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I am using the HOOMD-blue package, and I was advised to use force-shifted Leanard Jones potential, with a tree neighbor list. I do not know which parameters I should write for those charged molecules (hard spheres) "'N, charge'" The system would also have some counterions, and they have an impact on the system.
classhoomd.md.pair.ForceShiftedLJ(nlist, r_cut=None, r_on=0.0, mode='none')
nlist = hoomd.md.nlist.tree(
r_buff=0.4, check_period=1, d_max=None, dist_check=True, name=None)
Thanks in advance!
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Mohamed-Mourad Lafifi Thanks, those papers are useful, but they do not help me.
I did build the model, and I am struggling to apply electrostatic field to the model.
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I have created an Ice 1h structure and created an adhesive bond with the substrate in LAMMPS. Now in order to replicate an adhesion test, I need to detach it using a tensile force that pulls it away from the substrate. How can this be achieved? What fixes can be used for replicating this detachment mechanism? Any insight is appreciated.
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A universal testing machine, calibrated by existing measurements.
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Dear experts,
I am doing molecular dynamics simulation for quadruplex DNA and nickel Schiff base complexes with the workflow in attached picture. However, when I tried to generate the parameter files for Nickel complex using antechamber and tleap with GAFF in Ambertools 13 (step 2 and 3), there were major errors with the following announcements:
1.  For atom[27]:Ni, the best APS is not zero, bonds involved by this atom are frozen. The frozen atom type can only be 1, 2, 3, 7 (aromatic single), 8 (aromatic double) Error: cannot run
 2. Sourcing: ./leap.in
source: Improper number of arguments!
usage:  source <filename>
Could not open file frcmod: not found
Could not open file Ni1.mol2: not found
----------------------------
I used these commands for generating parameters:
 antechamber -i Ni1.pdb -fi pdb -o Ni1.mol2 -fo mol2 -c bcc
 parmchk2 -i Ni1.mol2 -f mol2 -o frcmod
 tleap -f leap.in
* The commands in leap.in file:
source leaprc.gaff
mods = loadAmberParams frcmod
N = loadMol2 Ni1.mol2
saveAmberParm N prmtop inpcrd
quit
----------------
Could you please give me some advices to fix these problems? I have attached the pdb file of nickel complex in case you need further information.
Thank you very much.
Kind regards,
Sean.
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hi dear
i am facing same problem. How you solved it ???
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I have a pre-equilibrated Ice 1h structure at 250K. I also have an Aluminium substrate which is 10 Angstroms below it within a simulation box. With the potential defined for structures (TIP4P for Ice, EAM for Al, LJ for cross-interactions), how can I bring both structures together to form an adhesive bond at the interface?
In terms of LAMMPS commands, how can this be achieved? Any insight is appreciated.
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Abhay Vincent in your model the LJ cross-interactions are the only ones between ice and Al, and the adhesion will be a consequence of them. Those are nonbonded pair interactions, so you don't need to create anything in terms of topology.
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Hi,
I am learning steered MD simulation for protein-ligand system. As I am a beginner in this method, I am trying to run the Lysozyme-ligand complex system described in the Bevan lab tutorial (http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html).
I have run up to constant pulling velocity step for the protein-ligand system. After that I have got a trajectory file which show that the ligand gradually coming out at a distance from the protein's active site due to the application of constant pulling force. After this step, I used the perl script available there in the tutorial which gives .gro files for each of the frames in the trajectory file.
After this step, I have 300 .gro files and protein-ligand distance containing .xvg files for each of the frames (attached).
After that, the tutorial described about the steps of umbrella sampling where individual MD run have to run for a number of .gro file from the frames. In the tutorial it has been mentioned that, the .gro files should be selected from a specific frame interval.
I have following questions at this point:
1. Which .gro files from the frames should I take for the umbrella sampling run and what is the logic behind selecting those frame?
2. Is this selection process vary with different protein-ligand complex? Or there is a specific trend?
3. What should be the total time scale for running each MD simulation of each .gro file during umbrella sampling? (for a protein-ligand system approx 350 residues)
4. What should be the configuration of CPU (How many core needed) for running umbrella sampling of a protein-ligand system?
Please help.
Attachements:
1. conf.gro.zip (all the .gro files for each of the frames)
2. dist_prot_lig.xvg (all the .xvg files corresponding those .gro files describing the distance between protein and ligand).
3. Summary_distance.dat (protein-ligand distance from the xvg files gathered in one document)
4. pullf.xvg (change of pulling force respect with each frame during the MD run)
5. summary_distance.png (plot of the Summary_distance.dat)
6. pullf.png (plot of the pullf.xvg)
Thanks & Regards
Manish.
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I have same question as asked my Manish
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I want to get a average structure from a pdb file containing multiple models. I used the command below:
gmx cluster -f input.pdb -s topol.tpr -cutoff 20 -method gromos -av
GROMACS Doc states that the ''-av'' option can ''write average structure of each cluster'', but how does it do it. I think there will be atom clash or unphysical residue structure if it is a simple average of atom positions, however, the result above seemed rational.
On the other hand, the GROMACS website also has a suggestion about average structure:
I am confused by the algorithm, and I wish someone can help me!
Thank you!
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I guess you are correct unless you describe the atom positions in center of mass coordinates, and more importantly, you have a system that has a very rigid conformation with small RMS deviations.
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Is there any way to construct different initial filler shapes like triangle, square, rectangle, pillar, and tube in any simulation software.
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Thank you @Wojciech Kopec.
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I have created an Ice 1h structure and am equilibrating it 100K in NVT ensemble in LAMMPS for a timestep of 0.25fs in 3000 steps. The potential used is TIP4P/Ice. Although the simulation runs fine without errors, the Ice 1h structure loses it's crystalline shape and atoms become disoriented inside the simulation box. Atoms are not lost but they just don't hold the hexagonal shape they are supposed to.
Is this supposed to happen or does it represent a problem with the geometry/potential?
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The initial geometry of the system is not related with the interaction force field (let's suppose that you have a good one and you have no mistakes in its implementation), therefore before to start the MD simulations you have to optimize the system geometry first. When you do the equilibration of the system you have to carefully produce the initial velocities (in old school, the initial velocities were zero, but the atoms were slightly displaced from their initial equilibrium position) in order to have no drift or initial tensions inside the system.
It is recommended to start the equilibration with a small systems, get it equilibrated, create a supercell of it (with the size what you are interested) and after that start the your simulation.
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Trying to simulate a ice-PTFE interaction and am unable to find a reference which actually lists out forcefield parameters for PTFE-PTFE interactions using ReaxFF or even other force fields like Dreidig, Tersoff etc. Any help is appreciated.
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T. P M Goumans Thank you so much for the reply.
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I am searching for tools to construct molecular beacons which shall be complementary to a given sequence. I don't want to design any primers. I found that UNAfold is one such tool which I could use. However, I am unable to download it. The server is consistently down. Please help.
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I am able to access it through http://www.unafold.org/
There appears to be no access issues currently.
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I am working on molecular simulation of adsorption and I want to design a new molecular simulator software by C++.
The input of this software is some text file. I want to get initial position of each atom in Cartesian coordinate in a text file.
So I want to make this initial position data.
Can I make a structure in Material Studio 2017 and convert/export or extract this data to a text file?
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You can export the Materials Studio generated structure into .car format. It will give you the coordinates of your structure in txt format.
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Is it possible to transfer heat from one group to another using simulated aneeling technique in the Gromacs software? I would like to transfer heat from a gold nanoparticle (group 1 from 310 to 350 K) into a dppc bilayer (group 2) that is at 310 K. How can I do it using a NPT ensemble in a molecular dynamics?
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You can define gold nanoparticle and dppc bilayer as two individual temperature coupling groups, and set simulated annealing for group 1, but set tau-t of group 2 to -1 to avoid artificially maintain its temperature, you should be able to observe heat transfer phenomenon.
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I'm studying adsorption of CO2 on faujasite (FAU) and I would like to compare my data with literature. However, most of the published works have been shown the loading of CO2 on FAUs as molecules of CO2 per unit cell of FAU. The following reference supplied the composition of FAU NaY as Na56.Al56.Si136.O384 and it showed the equilibrium data of CO2 on NaY as molecules per unit cell. How can I convert these data to mmol per gram?
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According to Wikipedia unit cell is a cubic with side equal to ca. 24.65 A. The specific gravity value is also given (1.96). There is also information about void fraction (0.48). Including the Avogadro number should be sufficient to convert the units.
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Dear All,
I am good at MD simulations with AMBER, NAMD, Gromacs, Forcite... But not familiar with MC simulation. Could you suggest some MC simulation packages? I have to calculate the binding energy of copper MOFs and small molecules at different temperatures.
Thanks,
Xiaoquan.
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You may find MC simulator inside LAMMPS package.
There is another simulator developed by the same group, but specifically for MC and Kinetic MC simulations (SPPARKS).
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hey, i am here with two basic questions:
I want to perform some analysis on monomers of pentameric protein. There is HSD residue in my protein but when i am performing hydrophobicity related analysis on it, i am getting error for the particular protonation state : like there is no hydrophobicity entry for HSD. is it possible to rename HSD residue to HIS in .XTC and .tpr files?
my second query is i have to select monomer and lets say run g_rmsf on it. How can i rewrite a trajectory with specific atom residues (monomer only) here? I didnt add chain identifiers to pdb before simulation ( A B C D).
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First question:
You cannot rename a residue in the trajectory as the topology is saved in the topology file your provided to the gmx tool, e.g. the .pdb file or the .top file. You just need to put these topology file in the commend line to let the gmx tool to read it.
Second one:
As the first answer writes, you can make an index file and use thr trjconv tool of gmx to extract the specific trajectory for the selected residues. The make_ndx command and trjconv command in gmx could do this.
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I am newbie in this simulation, so i would like to see the simulation for Protein-ligand..
can anyone here suggest which software that is easy to use for newbie?
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These are 5 most commonly used softwares for MD calculations: GROMACS, CHARMM, AMBER, NAMD, and LAMMPS. All these software have some common features along with some unique capabilities. Some are them are open-source (e.g, GROMACS, and LAMMPS) and rest are either proprietary or commercial. For biological applications, GROMACS seems to more suitable, though I have never used it. For other applications, e.g., materials and fluids, LAMMPS is a great tool. I am using is for the past 4 years and found it very robust, fast, and well documented. Although the initial learning curve of LAMMPS is quite steep, I can assure you that its capabilities make it worth going through that learning phase.
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Can someone please simulate and explain these protein-ligand interactions for each of the ligands:
Please help me, it's urgent.
Protein
Ligands
I can be contacted directly at alirazashafqat@gmail.com
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Why dont you use some visualization software such as Chimera or ligplot+. Your query will be resolved.
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I have a problem. My system is MGDG bilayer and in this system membrane has curves. I want to analyze hydrogen bonds only in small part of the system. I want to check how many hydrogen bonds I have, how many water bridges I have etc.
I try several methods to do that:
1. I delete all lipids and water from my system by my script and I left an only a small fragment in which I want to analyze hydrogen bonds.
a) Then I use gmx hbonds to analyze:
gmx hbonds -f *.gro -s .tpr -num *.xvg
but I use tpr from the whole system and it doesn't work. when I write this command my terminal stuck
b) Another method I created index file by using gmx make_ndx and I use my *.gro file to make index file and this gro file has an only small number of atoms, so I have an index groups (for water and for lipid) from an only small fragment of my system.
Then I use gmx hbonds to analyze:
gmx hbonds -f *.gro -s .tpr -num *.xvg
It works, but I have a very little number of hydrogen bonds and I know why, because the new index file gives inappropriate atom number. For example, if in my old system my atom had 110100 index number, now he have 100, because when I make new index file from my gro file it started count from 1 (and my fragment for example has atoms which have atom numbers from for example 90000 to 100000 and 130000 and 140000
c) I use new .tpr file by using gmx grompp, but it's very boring and you need a lot of work if you want analyze hydrogen bonds from for example 100 .gro files from a different time of trajectory, because I need to change every time my topology, because I have gro files from different times of trajectory and for example one file has 61 lipids and 1512 SOL and another gro file has 58 lipids and 1632 SOL molecules
So maybe someone knows how to do this?
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Your problem with method B is that you used an index file generated from a reduced atom to index into the full atom set. However, the indeces do not have to match (they wont once you have a gap in your atom selection). You can use your original tpr or gro file (of the whole system) to generate an index file with gmx make_ndx or gmx select and create index groups containing only the part of the system you want to analyze. Then use these small index groups as input for gmx hbonds with the whole system trajectory.
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It is difficult for us to directly observe the digestion process of food in the human gastrointestinal tract. However, molecular simulation is a powerful tool for us to explore the unknown world. We wonder whether molecular simulation can visualize this process?
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Molecular simulations is a powerfull tool for processes at atomic and molecular level, but you have to bear in mind that the length-scales and time-scales that are accessible for molecular simulations, provided you use supercomputers, are around a few tens of nm and ns-ms (small systems - longer time and viceversa). And then you have to have more precise questions before your set up the simulations (like "how protein A bonds to enzyme B" or something). Just throwing everything in a simulations box to see "what happens" is rarely a good idea.
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I am working with molecular simulation and modelling, and searching some softwares.
The most used software are Materials Studio and LAMMPS for Moleclar for Molecular Dynamics.
Is there a site/document that talks about it?
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Sorry, I have trouble understanding your statement.
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I recently updated to macOS 10.15 only to realize after the update that Catalina can only run 64-bit apps. VMD software often used in our group for visualization  only exists as 32-bit (https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD)
I cannot downgrade my OS version as that required cleaning up the hard disk.
What is the way around this? Has anyone faced this issue? Any suggestions 
#VMD
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Now there is a tentative build of VMD for Catalina:
Kudos to François-Xavier Coudert!
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I want to generate some random coordinates using Gaussian distribution function in MATLAB and import them into Materials Studio. Is there any tool available for doing this?
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Yes I already did the same steps but when I imported the new coordinates I found the bonds were broken. Is there any option inside Materials Studio to generate random rough surface using Gaussian distribution function?
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I was trying Oplsaa, which worked fine for me for polyethelene. But in the case of PS I had problems because grompp produced many warnings the same type: "No default Angle types, using zeroes". These errors concern the topology file, the part with 3-body angle. The problem is not connected with all atoms, but only one specific C atom in each styrene monomer: the one that connects the backbone with the phenyl ring. Each styrene part produces 3 warnings like above for C4-C3-C8, C3-C4-H and C3-C8-H interaction. I did not notice any other warnings.
Below I made bold the parts which produced warnings
           C1-C2-
                  |
                 C3
             //        \
      H-C4        C8-H
           |            ||
          C5        C7
            \\         /
                 C6
Can I then use oplsaa for PS in Gromacs?
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The molecular simulation of two 50 amino acid long helical proteins forming heterodimer has ran 100ns then again ran for 50 ns. But the RMSD graph deformed. I have used gromacs 5.0 and saved it nopbc.xtc format . The graph is attached below. Kindly help me!
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i think you should draw your graphs using xmgrace or matlab then it will be more clear.
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for example, I have used POPE cell membrane in my research work (molecular dynamics), but according to the paper that I attached below, this membrane is a kind of normal membrane.
if there is somebody who knows how to modify this membrane as a cancerous membrane, please recommend me.
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I would suggest you to look for a litterature about the lipid composition of cancerous cell membranes. POPE is just a model-membrane which does not need to be a representative for a cancerous cell membrane. Moreover, from the behaviour of compounds with the membrane composed only of POPE lipids you can not draw conclusions of the behaviour of cancerous cell membrane. To do more accurate research you shall also keep in mind what kind of cancer you are dealing with? In what tissue? Depending on tissues you will find the lipid composition which you need.
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I'm a very much beginner in using RASPA. I want to simulate a crystal phase, for which I have .xyz file. Can RASPA read .xyz files?
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You can use openbabel to convert structure files from one format to almost all possible formats with a simple command such as this:
babel myfile.xyz myfile.cif
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I wrote an MC algorithm that simulates bead-spring models and am in need of verifying the results of my code. Is there any resource in the literature that has energy expectation values (or any other metric) for MC simulation of bead-spring models that I can use for result verification?
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I appreciate your answer! I wasn't aware that that could be done for anything but the simplest models. I will look into this! Zhaoxi Sun
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recently, I encountered an error at the beginning of the simulation, which related to Atom 3662,
please let me know the solution of this error:
FATAL ERROR: Atom 3662 has bad hydrogen group size.  Check for duplicate bonds...
by the way, I didn't find a duplicate bond in the parameter file and I want to know, what's the meaning of hydrogen group size?
is it possible to know the root of this message?
best regards,
soroush
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thanks, Dr.coban,
I have solved this problem.
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How to create pressure differences across the membrane during NF membrane simulation by Material studio?
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thanks, but I could not understand your answer.
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1ns/hr for a 60k atom system unrestrained... GROMACS 2019... 1.0nm cutoff and 0.14 fft spacing...
160ns approx in 9 days... Count the power outage (totalling almost 9-10hrs last week), 3hrs rest per day...
Bad??? I don't think so... Any opinion???
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I find post MD 'analysis' more time consuming that pushes your limits to know more and more about your system in order to come out with something meaningful.
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Dear all,
I generated topology of a ligand (ATP) using Acpype which gave me the topology file topol.top and conf3_GMX.itp. I'm writing a report and confused as to what I should write in the report, "I'm using GAFF force field for ATP" or "OPLS/AA force field for ATP". The top line of the topol.top file says #include "oplsaa.ff/forcefield.itp" which caused the confusion. Although the conf3_GMX.itp file seems to have everything and I don't think Gromacs is taking any parameters from "oplsaa.ff/forcefield.itp" file but still I want to be sure. I have attached the topol.top and conf3_GMX.itp file.
My system has only ligand (ATP) and water.
Thanks and Regards,
Raghav
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Hi Raghav
ACPYPE generate the topology and parameter file for the small molecules with force fields like AMBER99SB or GAFF. The topologies generated according to the format of GROMACS (<file name>_GMX.itp, <file name>_GMX.top, <file name>_GMX.gro), OPLS (<file name>_GMX_OPLS.itp and same), CNS (<file name>_CNS.top and same). Thus without breaking the compatibility of the force field, the topologies generated can be used in AMBER force field or OPLS force field as ported in the GROMACS.
In your case, you have selected the itp file of the GROMACS format and top file of the OPLS format.
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In the molecular simulation in the Dmol3 program, some of the reaction paths have two-step intermediates. How can we recognize these situation ?
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if you have two negative frequencies you must choose the one that seems correct et run a TS optimization c est ca qui te Donne le vrai path
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Dear researchers,
I want to perform a DFT simulation on a combined system including a crystal (MnO2) and an amorphous (water) structures. How can I apply boundary condition on it? Thank you.
Regards,
Mina
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The periodic conditions should be defined by the crystal part of MnO2.
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I want to build a topology of my structure (PLGA polymer). using pdb2gmx through gromacs. But I did get the error 
Fatal error:
Atom type Zn2+ (residue ZN) not found in atomtype database.
Although My .pdb file does not contain ZN2+ or ZN atom or residue. I am using oplsaa force field.
how can I rectify the error ??
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There are parameters for ZN in some force fields like gromos and charmm36m. You need not change anything in case of GROMOS96 53a5 or 53a6. In case of charmm36m, all you have to do is change the name of the residue to ZN2 from ZN and it will work just fine.
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Dear all,
I want to generate the topology for ATP(Mg2+) complex using OPLS-AA force field. For only ATP i used Acpype and it worked but when I used ATP(Mg2+) acpype is not working, that's because antechamber use GAFF force field and it doesn't have Mg parameters.
Is there a way I can generate the topology with acpype for ATP(Mg2+)? or Is there any server that can give me the topology that i can use in Gromacs simulation?
Regards,
Raghav
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You don't need to parametrize Mg2+. Every force field already has parameters for it, and the parameters for ATP should not depend on Mg2+ at all, anyway, as doing so would create non-transferable parameters.
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Dear all,
Where can I get the structure of ATPMg+2 complex for my simulations? I need a starting structure for my MD simulations.
Thanks and Regards,
Raghav
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Scroll down to paragraph 2 with name "3D Conformer".
Under the text "3D Conformer of Parent Compound Adenosine Triphosphate (CID 5957)" (that give you hint where from this conformer was taken) - you will see 3 buttons with very promising names and pictograms.
If your software unable to open any of 4 formats they suggest you to, you can manually edit for examole SDF to XYZ, it take approx 1 minute.
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I'm doing the protein-ligand complex tutorial and when I'm going to convert the .str file to gromacs format with this command "python cgenff_charmm2gmx.py JZ4 jz4_fix.mol2 jz4.str charmm36-nov2018.ff", I get the following error. I Already use python 2,7 and I use a SSH secure shell to communicate with the server that works with the linux operating system Please, I appreciate your help and prompt response.
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Hello Fernel,
It looks to me like the environment you're using doesn't have numpy available which is used extensively in the package, or your system variables are not set up properly to find that package when calling "import numpy".
Are you sure it's been installed on the system? You can simply try, 'pip install numpy' while in the shell, and see if that fixes the discrepancy. This will depend on the setup of your machine. If you're on a cluster you may need to setup or activate a virtual runtime environment that has python and all the necessary dependencies.
Hope this helps and good luck!
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Dear all,
In gromacs tutorial its written that pdb2gmx can be used for cofactors like NAD(H) and ATP, my question is how can i use it on my pdb file of ATP molecule. Do i need to change the residue name? Right now I'm getting the error of unknown residue type LIG.
I want to generate topology files for MD simulations using gromacs.
I have attached my ATP pdb file. Looking forward for a reply.
Thanks and Regards,
Raghav
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These are the force fields that natively support ATP in GROMACS:
$ grep "ATP" *.ff/*.rtp
charmm36.ff/merged.rtp:[ ATP ]
gromos43a1.ff/aminoacids.rtp:[ ATP ]
gromos43a2.ff/aminoacids.rtp:[ ATP ]
gromos45a3.ff/aminoacids.rtp:[ ATP ]
gromos53a5.ff/aminoacids.rtp:[ ATP ]
gromos53a6.ff/aminoacids.rtp:[ ATP ]
gromos54a7.ff/aminoacids.rtp:[ ATP ]
As stated above, if you want parameters for other force fields, you will need to obtain them from another source.
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I want to know if there is an online server for ligand-protein complex docking with another protein. The available renowned protein-protein docking servers like ClusPro, HADDOCK, PyDock etc. either remove or give an error when I try to upload the ligand-protein complex as the receptor pdb file. How can I verify that binding of a ligand to a receptor induces a conformational change or directly blocks the interacting surface in which the native proteins couldn’t bind effectively thereafter?
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Ardavan Abiri If i understand correctly, you have a protein-A with bound ligand and you wish to dock another protein-B to this ligand-protein complex.
Well its true that protein-protein docking softwares do not handle ligand well.
Now i am presuming you have two conformations of protein-A :- (1) its native state and (2) protein-A bound to the ligand which has undergone a conformational change upon binding.
In such cases you can first dock protein-A (native state) with protein-B and predict the interface. Then you can dock the alternative conformation of protein-A with protein-B.
You can then compare the top predicted interfaces between the two types of docking experiments. If the ligand disrupts the binding, then this comparison of docking experiments might provide an indicator.
hope this helps.
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How to commence simulations in nanoscale? In which part of the code do we introduce the nano dimensions?
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Okay - so the question is how does my nanoparticle affect urea-water interactions?
Practically, to build the topology, the simplest way (for me anyway) is to have your nanoparticle parameters in a .itp file, then build your topology with something like:
#include "FORCEFIELD NAME.ff/forcefield.itp"
#include "nanoparticle.itp"
#include "urea.itp"
#include "tip3p.itp" (or whatever water model is appropriate)
[ system ]
Nanoparticle and urea in water
[ molecules ]
Nanoparticle X
Urea Y
SOL Z
Chapter 5 of the Gromacs manual has very detailed instructions on how to build topologies.
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Dear all
I have a molecular system containing metal ions in which reactions are occurred. Can I use ReaxFF force filed instead of performing DFT simulation? Can ReaxFF force field be used in ionic systems?
Regards
Mina
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Of course but you need a fully tested and reliable ReaxFF parameters.However, I strongly recommend you to apply AIMD simulation if it is applicable.
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I thinking of starting active research in molecular simulation with the goal of producing high impact papers. Do I necessarily need a supercomputer or a good intel xeon workstation with a high end gpu will suffice.
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The hardware and software needed for MD simulations depend on what you are trying to achieve. In general, fast hardware can produce long MD trajectories in less time than slow hardware. You can check specifications and standard benchmarks on various web sites to see how MD codes scale according to such parameters as number of CPU cores, number of GPU cores, and clock speeds of CPUs and/or GPUs. In my own case, I use YASARA-Structure for MD simulations, which combines CPU processing with GPU acceleration using OpenCL. With an Intel i7 CPU running at 4.4 GHz and an Nvidia GTX1080Ti GPU, I can get 350 ns/day in the DHFR benchmark in explicit solvent.
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I want to perform molecular dynamics simulations of a system with toluene solvent represented by TraPPE-UA (7-site) model using GROMACS-5.1.4. It is a rigid model and therefore has no intramolecular interactions. In the [ constraints ] directive of the itp file for toluene (attached here), along with 1-2 (and 2-3) distance constraints that rigidify bonds, I specify 1-3 distance constraints to rigidify 1-2-3 angle. If my understanding of the GROMACS manual is correct, such 1-3 constraints are called coupled-angle constraints and LINCS algorithm should not be used with them. SHAKE algorithm cannot be used with domain decomposition. Please suggest if there is a way to run parallel simulations using SHAKE algorithm. If it is not possible, please suggest a method to fix all the bonds and angles in a toluene molecule without using SHAKE.
Thank you all in advance.
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Just use mpi. What is thr difficulty here?
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Dear all,
I am trying to find Crystallographic Information File (CIF) of delta-MnO2 but unfortunately I could not find that. Can anyone send me .CIF file of delta-MnO2?
Regards,
Mina
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Mr. Sedighi,
You can use:
The cifs can be downloaded free of charge.
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Dear all,
I have this cp2k output file from a MD run MD-pos-1.xyz which has iteration number vs atomic coordinates information. I want to calculate charges for each atom for each iteration number. Is there a way to do this automatically? I tried running a single point calculation with the above MD-pos-1.xyz in cp2k but it considers only i=0 configuration and stops. Looking forward for an answer.
Regards,
Raghav
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Dear friend, Raghav Saxena.
If you use the “REFTRAJ” keyword in your calculations in CP2K to follow your trajectories, then you might look at these keywords: FIRST_SNAPSHOT, LAST_SNAPSHOT and STRIDE.
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Dear all,
I need the pdb structure of porcine skin gelatin or collagen, but I coul not find it anywhere, even in PDB data bank. How can I extract PDB structure file of this material from XRD data?
any help will be appreciated.
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Dear Dr. Honegger,
Thank you for your complete reply. Do you mean collagen is representative of gelatin? Evan though in the fragments of collagen some amino acids of gelatin are not exist?
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I am running the MD simulations for 30 ns which is 15000000 nsteps using dt= 0.02 using GROMACS software but it has terminated (after 13000000 steps) before completion due to queue limits. I would like to continue the same calculation to complete the 30ns simulation. 
How should I proceed?
According to Gromacs tutorial/manual, I should use -maxh option of mdrun to continue the terminated Job.