Molecular Simulation - Science topic
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Questions related to Molecular Simulation
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?
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?
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.
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?
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
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.
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=, y=, z= 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
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.
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
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
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.
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,
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
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?
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.
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 .
# opt=maxcycles=500 b3lyp/3-21g scrf=(solvent=dichloromethane)
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?
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.
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.
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.
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.
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.
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.
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 !!
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?
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 (
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?
Hi, I'm trying to do a simulation of my docking results and i got this 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
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?
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!
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.
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: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:
mods = loadAmberParams frcmod
N = loadMol2 Ni1.mol2
saveAmberParm N prmtop inpcrd
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.
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.
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?
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
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!
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?
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.
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.
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?
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?
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?
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.
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).
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?
Can someone please simulate and explain these protein-ligand interactions for each of the ligands:
Please help me, it's urgent.
I can be contacted directly at firstname.lastname@example.org
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?
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?
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?
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
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?
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
Can I then use oplsaa for PS in Gromacs?
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!
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.
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?
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?
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?
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,
In the molecular simulation in the Dmol3 program, some of the reaction paths have two-step intermediates. How can we recognize these situation ?
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.
I want to build a topology of my structure (PLGA polymer). using pdb2gmx through gromacs. But I did get the 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 ??
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?
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.
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,
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?
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.
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.
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.
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.
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.