Science topic

Computational Biophysics - Science topic

Explore the latest questions and answers in Computational Biophysics, and find Computational Biophysics experts.
Questions related to Computational Biophysics
  • asked a question related to Computational Biophysics
Question
5 answers
Greetings,
I have a computational biophysics background and I want to enter the field of Deep Learning. How can I do this? should I read books, research papers, etc..?
I know how to program in Python and I have taken some online courses on Coursera about Deep Learning so I have some basics, however, the courses were general and not based on biology problems. Therefore, I want to start learning it again in a more scientific way to do my PhD in it.
What are your suggestions? and is it possible to self-learn it or do I need a supervisor?
Thanks
Relevant answer
Answer
Dear Ibrahim, deep learning is only a suggestive word for indicating multi-layers neural networks, I totally agree with Thomas: there is no specificity of biomedical problems with respect to other pattern recognition problems. The specificty is linked to the need of 'explainability' : we cannot accept 'pure black box' solutions in a field like biomedicine that present an high 'context dependence' and this point is of utmost importance. You must privilege the possibility to give a biologically sound explanation to the output with respect to the mere prediction accuracy, see:
for some examples.
  • asked a question related to Computational Biophysics
Question
4 answers
Hello all
Is there any reliable and free web server that runs molecular dynamics simulation of proteins?
Relevant answer
Answer
These days journals demand for 100 ns and Online tools are not reliable for MDS. The best solution for MDS is always gromacs or schrodinger.
  • asked a question related to Computational Biophysics
Question
1 answer
When observing elastic modes of proteins, one of the results files shows deformation energy plot. What is the significance of deformation energy when studying protein dynamics?
Relevant answer
Answer
Deformation energy measures the rigidity of protein residues. Higher the Deformation energy, higher the rigidity residues have. Also, it gives idea about protein's local flexibility.
  • asked a question related to Computational Biophysics
Question
3 answers
Dear all,
I'm in principle a NAMD user but I'm new in performing MD simulation using polarizable force field. I wonder if anyone can suggest any MD software (NAMD or GROMACS, or ..) to implement polarizable force field easily and straight froward?
Thanks for your help,
All the best,
Zeynab
Relevant answer
Answer
Hi,
I recommend to you to take a look in the paper
Annual Review of Biophysics Polarizable Force Fields for Biomolecular Simulations: Recent Advances and Applications
Zhifeng Jing et al. Annual Review of Biophysics, 2019 https://doi.org/10.1146/annurev-biophys-070317-033349
  • asked a question related to Computational Biophysics
Question
4 answers
While am running the EM, the minimizatin gets stopped before the forces get converged at step 14
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 50000
Step= 14, Dmax= 1.2e-06 nm, Epot= 1.84916e+18 Fmax= inf, atom= 7809
Energy minimization has stopped, but the forces havenot converged to the
requested precision Fmax < 1000 (whichmay not be possible for your system).
It stoppedbecause the algorithm tried to make a new step whose sizewas too
small, or there was no change in the energy sincelast step. Either way, we
regard the minimization asconverged to within the available machine
precision,given your starting configuration and EM parameters.
Double precision normally gives you higher accuracy, butthis is often not
needed for preparing to run moleculardynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)
writing lowest energy coordinates.
Back Off! I just backed up em.gro to ./#em.gro.9#
Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 1000.
Potential Energy = 1.8491607e+18
Maximum force = inf on atom 7809
Norm of force = inf
What should I do?
Relevant answer
Answer
@Richard Mariadasse can you suggest me how do you solve the problem?
I'm having the same issue
  • asked a question related to Computational Biophysics
Question
5 answers
A number of post translational modifications can occur to a protein, including phosphorylation, methylation etc. I am aware that there are a number of servers and tools to predict positions for these modifications based on sequence and/or structural patterns or motifs. However, is there a tool (or server) available that can actually model them on a structure (or a model)?
Relevant answer
Answer
Hello,
If you want to add a post translational modification in an existing pdb file You can try Vienna 2.0
Best,
Christophe
  • asked a question related to Computational Biophysics
Question
12 answers
INVdock software has been used to predict the first receptor of drug with low molecular weight and finding or predicting cell target, I would be thankful to anybody who could let me know how could I get the software and procedure for working with the same.
How is the popularity of INVdock software?
is this software free and what is the procedure of working with that?
Relevant answer
After all that time, unfortunately, it still unaccessible.
Kindly see the attached file and the link below:
Regards
  • asked a question related to Computational Biophysics
Question
5 answers
Dear all, 
I'm running simulations on membrane proteins (POPC) using Desmond software and I would like to use GROMACS tools to analyze certain parameters related to the membrane. Exemple:
- Deuterium order parameters of the acyl chains
- Density of the membrane environment
- Area per lipid headgroup
- Bilayer thickness
- Lateral diffusion of the lipids
Some files are easy to generate using VMD (.trr, .gro files) but I'm having difficulties to generate a tpr file.
Could you help me with any available tools please.
Thank you in advance for your help.
Zeineb
Relevant answer
Answer
some idea I got from the above discussion.. actually I have a Desmond trajectory, for that opls2005 ff was used. Now I want to calculate g_mmpbsa. for that I need a .tor file... can u plz tell me shall I use vmd to convert mywhole_out.cms+click.dtr>mywhole_trj.pdb then using that .pdb how to generate .tpr??
  • asked a question related to Computational Biophysics
Question
3 answers
Few of us wanted to create a discord server for Biophysics. What we intend is to begin a commonplace for discussions/numerical experiments. Also possibly document the results in the form of blogs or other media.
I believe that there are many biophysics/computational biophysics/Molecular Dynamics enthusiasts here. Here is the server link: https://discord.gg/qRQRq2k
Come and join us. Let us learn together.
Relevant answer
Answer
Dear Devanand,
Can you explain more what is the purpose of this post and what the discord means?
Bog
  • asked a question related to Computational Biophysics
Question
4 answers
Hi All, I am trying to simulate one DMPG lipid bilayer in interaction with some fusion peptides. First I am preparing the membrane, and I am facing the problem: How to enable the NAMD to use NBFix parameters for SOD ions? Does anyone know how to set up this using NAMD and Charmm 36 FF?
Thanks in advance!
Relevant answer
Answer
Hi, now do you know how to add NB-fix or change it in the NAMD simulation? I am faceing the similar problem as you? Thanks a lot!
  • asked a question related to Computational Biophysics
Question
14 answers
My protein is 476 residues. I would like to plot the map only for specific regions and mention it in the input thus choosing the residues i wish to calculate the contacts for. Does anyone know of any server /standalone programs for same?
Relevant answer
Answer
Try using LigPlot+ or Discovery studio.
  • asked a question related to Computational Biophysics
Question
5 answers
I am working on computationally understanding the active and inactive conformations of some proteins. Simulating the inactive conformation from the active conformation is reported in literature by performing enhanced sampling MD studies, like Metadynamics, REMD etc., in which energy is added in particular co-ordinates called collective variables. This makes it slightly biased.
If I run unbiased atomistic molecular dynamics simulations of several microseconds, will my protein explore the conformational space by crossing the energy barriers? Or will the system be eternally stuck in a local minimum which it first reaches?
Relevant answer
Answer
Hi Rajiv,
It depends on the system you are studyng, some systems dont show important conformational changes in the microsecond or even in the milisecond time scale not only because they get trapped in a local minimum but also perhaps the conformational change is coupled to protonation or deprotonation or by some physicochemical conditions (pH or temperature). Therefore, before planning a computational experiment you need to search enought informatation about your system to propose the experiment.
If you ask me, I prefer run unbiased atomistic molecular dynamics simulation in the microsecond time scale, than biased methods for the reasons that you mentioned.
  • asked a question related to Computational Biophysics
Question
5 answers
Hi!
So far I have been preparing my MD systems for NAMD using Modeller and CHARMM-GUI. I am thinking about switching to Schrodinger suite of programs. To perform MD I am using a supercomputing center not supporting Desmond. Is it possible to (without any complicated modifications) use systems (homology models with ligands, lipid memebranes etc) build in Maestro in NAMD?  
Relevant answer
Answer
I suggest you prepare/equilibrate your system with NAMD. You will need binary coordinates, velocity and standard NAMD psf (CHARMM-GUI xplor_ext.psf). Then you can use GARDEN/VIPARR option of DESMOND to properly create and then link DMS files required for DesMOND runs. VMD will output initial DMS and then you simply link it to parameters needed. Something like this would work nicely:
viparr -f charmm36_aminoacids -f charmm36_lipids -f charmm36_ions_nbfix -f tip3p_charmm initial.dms mdrun-ff.dms
  • asked a question related to Computational Biophysics
Question
7 answers
Hello!
For instance, in MD simulation of the the interaction between a peptide and a metal ion (like Zinc ion, Al ion, Mg ion etc.), does it possible to define the peptide as ligand and the metal ion as receptor?
Relevant answer
Answer
The binding free energy is the free energy difference between the complex and the two isolated components. This is independent of which of the two components you call receptor and which you call ligand.
  • asked a question related to Computational Biophysics
Question
5 answers
Dear All,
I have an amino acid interacting weak with a CNT. During the standard MD it adsorbs, desorbs and then re-adsorbs on the CNT surface. Which method does suits to calculate the adsorption energy? Is there any fast and easy way to calculate the adsorption energy?
Thanks in advance,
Zeynab
Relevant answer
Answer
Dear Zeynab,
I think you could estimate the adsorption energy by picking the absorb and desorb structures and minimizing them. If those structures are stable enough you could obtain each energy state by minimizing them. I don't know how complex your system is, but I guess this could help.
Veronica
  • asked a question related to Computational Biophysics
Question
14 answers
Rather basic question for the experts. I have frames from 1.gro, 2.gro .....20.gro in order. I want to join them to a .trr or .xtc file to make a trajectory. How can i do it using gromacs commands. Thanks in advance 
Relevant answer
Answer
If you want to order a very long list of *.gro or *.pdb files you can place them on a single line in a file (list-pdbs-oneline.txt) and generate the timestep file (times-pdbs.txt) simultaneously:
Here is one I do when I have thousands of configurations to include:
#!/bin/bash
a=0; b=1;
for i in {1..10000}; do echo -n " trimer_${i}_${j}_${k}.pdb" >> list-pdbs-oneline.txt ; echo ${a} ${b} >> times-pdbs.txt ; let a=$((a+1)); b=$((b+1)); done
I can then run a trjcat:
trjcat -f `cat list-pdbs-oneline.txt` -o traj.xtc -settime < times-pdbs.txt
Works like a charm.
  • asked a question related to Computational Biophysics
Question
6 answers
Linear interaction energy
===================
How to define energy groups in protein ligand complex (solvated in water) and ligand in water?
Relevant answer
Answer
The initial LIE values were: alpha = 0.161 and beta = 0.500.
The refined LIE values, which distinguish beta according to net charge of, and number of hydroxyl groups in, the ligand (or probe in general) are: alpha = 0.18, beta = 0.500 (charged), beta = 0.430 (neutral with no hydroxyl group), beta = 0.37 (neutral with one hydroxyl group), and beta = 0.33 (neutral with two or more hydroxyl groups).
Neither alpha nor beta should be considered as a freely adjustable fudge factor. Large deviations from the initial (try first) or refined (see, if you get better results) values suggest a problem with the simulated model rather than with LIE parameters.
  • asked a question related to Computational Biophysics
Question
4 answers
Hi All,
I want to perform Molecular Dynamics (MD) simulation (using NAMD and CHARMM force field) of carbon nanotube/graphene with topological defect like Stone-wales. Creating topological defects changes the distance among carbon atoms from those using in pristine nanotube/graphene. I wonder whether I have to change the parameters like equilibrium distance and the spring constant value in the topology file or it isn't needed?
Relevant answer
Answer
If you use a good forcefield, you don't need to do that. Relaxing the system with the defects should give you the changed geometry.
If you want to study the properties of CNT/graphene itself, CHARMM is OK as a first try, but I wouldn't recommend it for an advanced study. It only contain harmonic bonds and angles. You might want to look at something like Tersoff-Brenner. If you want to study the interaction of the defected carbon nanostructure with something else, then CHARMM should suffice.
  • asked a question related to Computational Biophysics
Question
9 answers
Dear all,
I want to run the molecular dynamics simulation of an infinite graphene sheet solvated in water using NAMD code. I don't know how to create an infinite sheet with it's periodic images. Should I add bonds between graphene and it's periodic images or is not needed?
Would be so much thankful to help me..
All the Best,
Zeynab
Relevant answer
Here is the NAMD mailing list where Josh answered me exactly how to do that along with all details :
  • asked a question related to Computational Biophysics
Question
8 answers
Dear all,
I have performed MD simulation for different carbon nanotubes (CNTs) in water using NAMD software. Each CNT is solvated in a water box initially and MD is performed for each box. Is there any way to quantify which CNT is better soluble? for example calculating heat of solution? If so, how I can calculate it?
Thanks every body ..
Relevant answer
OK, Thank you so much for your time..
  • asked a question related to Computational Biophysics
Question
6 answers
Hi All, I started simulation of reverse micelles in gromacs. After simulation I tried to visualise my system in VMD (it look like fig min.RM.png), to visualise properly I tried trjconv tool in gromacs but unable to relocate with in box. So I check with starting system, my initial system are not in the  center to box (see fig: pack.png)
Is there any way to visualise my system
Thanks
Relevant answer
Answer
Trajectory files need some process before using to extract information.
Trajconv is used as an editing tool for the trajectory file to correct periodicity or modify the trajectory file manually like time unites,frame frequance, etc). Through the MD , the protein diffused in the unit cell so it sometimes jump from one side of the unite cell to the other side. So the following commands used to correct this:
gmx trjconv -f md_0_50_raw.xtc -s md_0_50.gro -o md_nojump.xtc -center -pbc nojump -n index.ndx
then type 0 | 0 ,
gmx trjconv -f md_nojump.xtc -s md_0_50.tpr -o md_0_50_processed.xtc -center -pbc mol -ur compact -n index.ndx
22 | 0
22(represent the protein option)
  • asked a question related to Computational Biophysics
Question
11 answers
I had run MD simulation with NAMD and want to check the differences of R of G during the simulation time. Is it important and efficient to record R of G? or there is another parameter that I should calculate?
Thanks
Abdo
Relevant answer
Answer
So the rog_loop_dcd.tcl I uploaded before had a minor issue. I am updating the code here based on Abdo's reply. I am happy if this helped you. (I have updated the code above also. The changes are given below also)
source gyr_radius.tcl
source center_of_mass.tcl
set outfile [open radius_of_gyration.dat w]
puts $outfile "i rad_of_gyr"
set nf [molinfo top get numframes]
set i 0
set prot [atomselect top "protein"]
while {$i < $nf} {
$prot frame $i
$prot update
set i [expr {$i + 1}]
set rog [gyr_radius $prot]
puts $outfile "$i $rog"
}
close $outfile
  • asked a question related to Computational Biophysics
Question
10 answers
I was trying to simulate a 512-DPPC membrane after developing it from Tieleman's model of 128-DPPC bilayer. I removed the initial periodicity and the water molecules using trjconv as suggested by Justin Lemkul in his tutorial of membrane protein simulation (KALP15 in DPPC probably). I used genconf to place the 128-DPPC membrane sidewise in a 2(x) 2(y) 1(z) format.
The first picture i.e. of nice bilayer is after energy minimization using a steepest descent algorithm with a gradient of 100 kJ/mol/nm. It is only after NVT equilibration with a high position restraint applied on the DPPC residues, it is making a hole inside the membrane i.e. the bilayers tear apart.
I tried this several times changing the temperature (to change the membrane fluidity) and the gradient too (I primarily used 500 kJ/mol/nm and then reduced it to 100).
Any idea on how it can be solved? I see quite a few water molecules inside the bilayers which go out during equilibration. Also, the ions show a tendency to make a cluster at one corner of the membrane.
Please help...
Relevant answer
Answer
I assume in the second figure, you have used unwrapped trajectories. Then,
to me, it seems like an in-plane pressure build-up problem. Have you tried applying a barostat, either isotropically or just in-plane? You have done an energy minimization first, which corresponds to minimum potential energy and equilibrium at 0 K; but when you apply a finite temperature, the membrane undergoes thermal expansion. With the fixed box size in an NVT simulation, it is reasonable to assume the membrane will "buckle" the way it seems it does.
  • asked a question related to Computational Biophysics
Question
8 answers
I want to predict the protonation states of Histidine in my protein and I don't have any ligand. As long as I try Propka 3 (only protein) and Propka 3.1 (protein and ligand), I receive different results and I'm wondering which one is trustworthy. Can anybody help? Thanks.
Relevant answer
Answer
You can use the ProteinPrepare web application (www.playmolecule.org) for protonation prediction and structure optimization. We use PROPKA3.1 as well.
  • asked a question related to Computational Biophysics
Question
3 answers
I'm trying to study my protein in different pH conditions (using Gromacs) but how can I change the protonation state of some residues of my protein to mimic different pH? I have already used H++ but cannot proceed.
Relevant answer
Answer
Take a look at ProteinPrepare application (www.playmolecule.org), you can predict protonation at desired pH, force any protonation you want and generate a pdb with corresponding hydrogens.
  • asked a question related to Computational Biophysics
Question
9 answers
Visualizing protein folding in gromacs
Relevant answer
Answer
Yes, DSSP tool is in gromacs but don't know is it gonna work in your PC or not. In my case, it is installed in super computer facility, so I use it without any problem. When I try to use it in my PC it shows some kinda error related to executable file.
  • asked a question related to Computational Biophysics
Question
9 answers
Hi Everybody,
Wish somebody help me to understand the following situation: Consider the MD simulation of two interacting molecule (first one on the left and the second one on the right) in a unit cell: The second molecule is interacting with the right side of the first one. Then, the second molecule start to get far from the first one and to get out of the unit cell, lets say the right-hand face of unit cell. Under the PBCs it has to enter from the the left-hand face and it interacts with the first molecule from the left side of the first molecule, while before getting out the cell it was interacting with the right side of the first molecule. I wonder if such simulation is correct...? I mean before getting out of cell the second one was interacting with the first one from its left side and if it interfaces the cell wall, it interact with the first molecule from its right side. There is a jump and I don't know how to deal with that during the simulation..  
Relevant answer
Answer
It depends on the range of the interaction and the size of the system. In case of long range electrostatic interactions, a particle will strongly interact with more particles within the unit cell and in the neighboring cells and it would be very expensive to compute these interaction directly. Thats why ewald sum methods are used. 
  • asked a question related to Computational Biophysics
Question
8 answers
I am simulating Protein-ligand interaction using gromacs and now I am getting this problem. Please held how to fix it.
Fatal error:
Too many LINCS warnings (1001)
If you know what you are doing you can adjust the lincs warning threshold in your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem
Welcome for your assistance.. my md.mdp file is attached
Relevant answer
Answer
Dear Alejandro, 
Thank you, how can I use soft-core potential, the problem still persist. please assist. 
Thank you
  • asked a question related to Computational Biophysics
Question
3 answers
I am trying to simulate do a Umbrella sampling simulation in GROMACS. I have the starting structure from XRD. The ligand sits almost at the middle of the lipid bilayer. I want to generate the initial  configuration for performing US. I am stuck with what I should give as the reference so that the ligand traverses from the extracellular side to the intracellular side. 
Relevant answer
Answer
You have to define 2 groups f.ex center of mass of the bilayer and ligand. If you perform, pulling simulation, then ligands starts moving. It is easy to extract windows by means of a script for the umbrella sampling simulation. https://www.researchgate.net/publication/315788220_Phosphatidylserine_flip-flop_induced_by_oxidation_of_the_plasma_membrane_A_better_insight_by_atomic_scale_modeling
  • asked a question related to Computational Biophysics
Question
2 answers
The values of the dipole moments of the given purine tautomers contain in the range of 1 to 23 Debye. I've got also Hirshfeld partial charges.
Relevant answer
Answer
I meant potentiometric titration. 
  • asked a question related to Computational Biophysics
Question
2 answers
Hello all,
I would like to know how replica exchange umbrella sampling methods works , and how can i start by using plumed plugin to gromacs.
Thanks in advance,
Sincerely,
ANJI BABU
Relevant answer
Answer
thank you
  • asked a question related to Computational Biophysics
Question
4 answers
I have MOE software.  I can keep NAMD as exe from other source. I can run this. But problem is for 10 ns 20 ns or 50 ns simulation I don't know the simulation Protocol like sampling time, equilibration period or others. if any one have good recommendations and suggestions i will be really benefited.  
Thanks in advance. 
Relevant answer
Answer
You can download and install NAMD software and simply run Your simulation (manuals and tutorials are available, it is not a problem), using the force field You need and all parameters (which should be chaanged from by default mode - time, temperature, time step/iteration) - this is the first way, without MOE. If You are not going to run steered MD (with constraints invoved in fixing of the distance or freezing the group or even pulling of the structure part to any place in the 3D space...), the protocol will stay almost untouched. However, if You have an access to MOE You can also do the same, taking the tutor for NAMD while setting Your MD, and run it in MOE environment. That is all You need.
  • asked a question related to Computational Biophysics
Question
4 answers
i have done docking study using Patchdock and firedock of protein (pdb id 3F7Z ) with  ligand (gymnemic acid ) i got the result Global Energy - 62.74 ,( in autodock4 gave  -5.2 ).
when i am doing for the molecular stimulation with NAMD it shows
ERROR: Constraint failure in RATTLE algorithm for atom 848!
ERROR: Constraint failure; simulation has become unstable.
is it possible after getting good binding energy in docking then molecular simulation  become unstable ?
(Note: i have done with other protein (like PDB id :1c83, 1IRK ) with same ligand  i got good results  for molecular simulation ) 
Relevant answer
Answer
Does the atom ID 848 belong to the ligand or to the protein? Is it a hydrogen atom? Does it happen during the gradual heating of the system? Check the initial coordinates: make sure there are no close contacts: remove the close contacts by energy minimization or by hand. If this does not help, adjust the equilibration protocol: reduce the time-step.
  • asked a question related to Computational Biophysics
Question
5 answers
Hi everyone, I have a query to ask regarding molecular dynamic simulation by using Gromacs. When the running simulation was accidentally stopped, and re-run, should I need to type any command to combine the .gro file or any file?
Actually, I had run some simulation. The problem was, some of the graphs gave only 30ns (or less than 50ns) while, I am running for 50ns Md simulation. I have checked the .log file and found that the simulation was finished running for 50ns. Here, I attached the rmsd picture and the .log file for your reference.
Thank you.
Relevant answer
Answer
Did you merge both trajectories before calculating RMSD.
You can use
gmx trjcat -f 1.trr 2.trr -o final.trr
  • asked a question related to Computational Biophysics
Question
5 answers
I used gromacs to perform a 10 ns equilibration of POPC membrane. I've heard that we can use gmx density to get the bilayer thickness. I would be very grateful if anyone can suggest me how to use it to measure bilayer thickness. Thanks
Relevant answer
Answer
You may want to try the 'GridMAT' program. Here is the link:
  • asked a question related to Computational Biophysics
Question
5 answers
I am simulating Aβ peptide (2BEG) with inhibitor, how to add molecules at random position prior to solvation, which was done by lemkul in his study.
Relevant answer
Answer
 The easiest way to do that is to use packmol.
  • asked a question related to Computational Biophysics
Question
2 answers
Removed Question as account inactive and questions cannot be deleted
Relevant answer
Answer
Is xray data available? I assume you want to align the MD density to the crystal data. To do that you need to superpose your model onto the Xray model, then calculate Fmod using the superposed MD model in the unit cell of the xray data. With two isomorphous data sets you can inspect the density easily using Coot. You can create a difference Fourier using CNS tools or Phenix.
  • asked a question related to Computational Biophysics
Question
5 answers
I am simulating Aβ Protofibrils (2BEG), I want to cap N terminal, How to cap it, I acetylat  N-terminal in pymol, and pdb was edited for CH3 to CA and run pdb2gmx following fatal error given.
  Fatal error:
Atom CD1 is used in an interaction of type atom in the topology
database, but an atom of that name was not found in residue
number 5.
Relevant answer
Answer
U try to copy the force field from gromacs/share/gromacs/top/usded_force_field.ff to ur working directory and edit the LEU part (shown below) in aminoacid.rtp file. 
[ LEU ]
[ atoms ]
N N -0.31000 0
H H 0.31000 0
CA CH1 0.00000 1
CB CH2 0.00000 1
CG CH1 0.00000 2
CD1 CH3 0.00000 2
CD2 CH3 0.00000 2
C C 0.450 3 ;;                This is the carbon which you have to cap. 
O O -0.450 3
one thing u have to care.. whatever atom type u will use there, same atom type u have to use here. 
Note. Do not use any random atom type for that carbon because whatever atomtypes are assigned in atomtypes.atp file, that atom potentials are only available in force field. If u will use random atomtype, again u will get same problem.
  • asked a question related to Computational Biophysics
Question
6 answers
I am trying to do protein folding studies for approx 70aa length protein using Gromacs. However, when I perform simulations, my protein goes out of the box and interacts with its images when simulated at 1.00nm box.
Can anyone please guide me as to how to calculate (if there is a formula or so) how big the PBC box should be such that no interactions are allowed between the periodic images?
Relevant answer
Answer
You should determine the water box sizes based on the protein unfolded structure, using for example one of the unfolded configurations. Based on this unfolded structure, you can determine (x_max, x_min), (y_max, y_min) and (z_max,z_min) of protein. Then, construct a water layer around the protein with thickness at least the cutoff of non-bonded interactions size: let's say if the cutoff=11-12 Angstrom, then the thickness of the layer is 15 Angstrom (assuming that the water box may shrink a little if the water box is not initially equilibrated at normal conditions, i.e., density = 1 gr/cm^3). Then, the big water box sizes are defined as:
big_sizeX = x_max-x_min + 2*thickness
big_sizeY = y_max-y_min + 2*thickness
big_sizeZ = z_max-z_min + 2*thickness
Then, after building a water box with these dimensions (big_sizeX, big_sizeY, big_sizeZ), you can solvate the folded protein structure in this 'big' water box. With this, then, you are sure that even if the protein gets unfolded, the images will not see each other.
  • asked a question related to Computational Biophysics
Question
3 answers
i want to study the nature of protein dna interaction using charmm36, I face problem to generate the psf file of protein dna complex.
Relevant answer
Answer
I think you want PSF -- not PSFGEN --- 
psfgen is a plugin which allows you to generate psf files. 
psf files are protein system description files, also called structure files, which explain your system to the simulation engine. 
To generate a PSF file you can do two things -- 
1) rely on automated tools
2) use psfgen
given that you are new to this - I would recommend doing lots of reading and using one of the automated tools packaged within VMD called AutoPSF builder. you can use that to generate a PSF and a PDB file for your system of interest. It will work as long as the DNA consists of standard nucleotides and protein comprises of standard amino acids. Remember - to add the latest topology file before generating the PSF and PDB.
Hope this helps.
Best,
/A 
  • asked a question related to Computational Biophysics
Question
7 answers
Dear all,
I am doing QM/MM study of protein. Earlier, I have done solvation and equilibration by using CHARMM22 force field in NAMD and input file for QM/MM in Gussian 09. So, my question is that can I use AMBER force field in NAMD? And if yes then what is the step by step description for solvating and equilibration of protein structure?
 
Relevant answer
Answer
Yes, you can use Amber ff in NAMD, similarly to using charmm ff. You have to look at 'toppar' folder of charmm program for finding amber ff in the format accepted for NAMD. There are some changes that you have to do in the input configuration file of namd as explained in this link: 
You should pay attention to the 1-4scaling factor, which has to be changed now , as explained in the above link, (the default value is 1.0, which is valid only for charmm ff.)
  • asked a question related to Computational Biophysics
Question
13 answers
Hi everybody,
I would like to pull a ligand in a channel from my protein and calculate the PMF with Umbrella sampling. This channel is probably not linear and thus have to be refined. Too much colisions appears along a simple one axis pulling and causing a catastrophic PMF calculation.
Currently I'm working with Gromacs and I wondered if it is possible to define statically or dynamically the coordinates for the center of the channel and use it during the simulation (Pulling).
One solution could be to define in the md_pull.mdp configuration file all the transition points of my pathway through which my ligand must pass from my APO structure determined with CAVER.
Instantiation of Gromacs parameters of md_pull.mdp is not enough clear for me and PLUMED is may be a more direct solution. Currently I have no experience with PLUMED but It seems on paper to be able.
An other choice would be to define dynamically the channel center, on-the-fly. PLUMED seems also capable to manage this sort of challenge but once again I have no idea of the feasibility of a such work.
What do you think about this problem and of the tracks evoked above ? 
Cheers, FR.
Relevant answer
Answer
Hi Francois
None of the  magic recipes proposed with a lot of hype for calculating free energies of
such complex systems from  canned MD like Gromacs,Charmm and the like do not
survive a true statistical  physics examination  because concepts like entropies,chemical
and potentials are not quantities derived from Newton's laws which deliver only mechanical
quantities and time averages of them .In simple systems one ASSUMES that these averages are ergodic (strictly proved only for a system of hard spheres by Ya Sinai)  but
even this is not true for a protein-solvent-ligand system  with multiple time scales ,strong
long range electrostatic interactions and  a solvent like water.The major problem is not the
inaccuracy of the   force fields but the very nature of the quantity you want to estimate.It
would much better do  Monte Carlo Simulation but this is much more difficult for your system so nobody suggests or develops such and hides the garbage under the carpet in the name of quick success.A more modest approach would be to search for clever
approximate and  softer modelling combining physics geometry and experimental data.
Of cource it is always possible to believe in MacMD and run everything,  this is usefull
for many things and I have done it for decades myself but I  don't believe the free energy
results for systems like yours.
  • asked a question related to Computational Biophysics
Question
3 answers
Hello
    For learning purposes, I'm working on a simulation where the user can input any force equation and the application will apply that equation to all bodies on the simulation.
    For non-bonded atoms, I'm using Lennard-jones, but what should I use for the bonded atoms.
    For example. If I want to simulate a water molecule, I guess I should use the Lennard-jones for the H-H inside the same molecule, but which equation should I use for the O-H.
   Thank you -)
Relevant answer
Answer
@Drahomir, thank you. That is exactly what I was looking for in this specific case.
@Dikeos, thank you, I didnt know that part, it will help me a lot
  • asked a question related to Computational Biophysics
Question
3 answers
Dear all,
I am simulating a protein in solution, GROMACS 5.1, Verlet cut-off scheme.
I realised I put wrong charge groups in the topology file. I have read that with Verlet they are not considered but as a safety check I recompiled a tpr with the correct topology and run two simulation, from the same cpt file of an old one: one simulation continuing with the wrong set up, one with the correct.
The output is not identical (I run them on the same computer), but I am wondering if it is because of the charge groups or because with the new tpr I am introducing new sources of randomness. Can you help me? Or suggest a check to understand whether the charge groups are influencing the dynamics or not?
[in the tpr, original and new, gen_vel=no, continuation=yes, ld_seed=10 (same value)]
Many thanks
Relevant answer
Answer
Yes, as I said, Verlet ignores charge groups.
  • asked a question related to Computational Biophysics
Question
1 answer
Hi,
I want to know whether the flat-bottom position restraints can be applied only for the pull code in umbrella sampling or it can be use for NPT or MD simulation of GROMACS (not umbrella sampling), If yes, please guide me how to use.
Regards,
Swati
Relevant answer
Answer
Just a generall answer, if gromacs allows to set the exponent for any hamonic restraint you want to use, using a higher exponent than the usual 2 will also flatten the middle potential area
  • asked a question related to Computational Biophysics
Question
3 answers
I have seen many papers on folding and unfolding of peptides using Replica exchange with solute tempering (REST). How do we implement this method in GROMACS > 5.1?
Relevant answer
Answer
You might want to refer to the two papers linked below.
The first one tells you how to scale your force field parameters by specific factors; basically, you'll have to make local copies of your force field files and write a script to scale the parameters for protein atom types.
The second presents HREX, a patched version of Gromacs (AFAIK limited to 4.6, so it might not be possible to run REST in gmx > 5.1) that allows to perform replica exchange with arbitrary energy functions; from what I recall, the problem is that standard Gromacs has replex limited to the lambda code, so this workaround was necessary.
I assume you're fluent with Gromacs and scripting - setting up REST might not be as straightforward as, say, running standard REMD.
  • asked a question related to Computational Biophysics
Question
3 answers
Molecular Dynamic (MD) simulation is an effective tool to determine the movement of molecules and hence to predict the properties of suspension at interface.
I am facing problem to 1. generate code for the sample material, 2. Force analysis at interface.
Relevant answer
Answer
There are a lot of software packages available that are available that will probably work for what you are wanting to simulate. I think that LAMMPS, DLPoly, NAMD, Gromacs are all open source.
If you want to understand what these programs are doing I recommend that you pick up a copy of the following books (these are only two of many possible books on the subject)
or
Best of luck.
  • asked a question related to Computational Biophysics
Question
7 answers
SASA is the surface area of a biomolecule that is accessible to a solvent. If I define the amino acids forming binding cavity and measure the area of the surface, can that be considered as the total area available in that cavity or the area available for the inhibitor molecule...??
If yes, then can it be used to screen the inhibitors based on their total or topological polar surface area (TPSA)..??
Relevant answer
Answer
SASA is computed by assuming that it is the area traced out by a probe sphere that simulates the solvent when it rolls over the atoms of your macromolecule (protein). This sphere is usually given a 1.40 Angstrom radius because the solvent is normally water and that size mimics roughly a water molecule.
However, you can compute SASAs for probe spheres with different radii. Regarding your question, it must be assumed that both the protein and your inhibitor molecule are immersed in water and then the SASA area should describe both of them. Note, however, that SASA calculations consider no interactions (such as polarity effects) at all but they rather estimate (roughly) an area covered by a mere superposition of atomic spheres which have predefinite radii (van der Walls or any other scale).
Taking into account all of the above, I should consider the SASA area of the cavity as the total area available in that cavity.
Nonetheless, I recommend you some more reliable methods to estimate sizes of binding cavities in proteins: CAVER, CASTp, and DogSiteScorer (links provided below)
  • asked a question related to Computational Biophysics
Question
5 answers
Dear All,
I have tested with two ways of solvating a peptide with urea-water mixture in Gromacs.
Method 1: Pre-equilibrating a urea-water box and solvating the peptide with -cs option with this box
Method 2: Adding urea molecules to peptide box using -ci option and then solvating the resulting box with water molecules
In both the methods, same number of urea and water molecules were added . 10ns equilibration followed by 20ns simulation steps were carried out.
On analysing the properties, average number of hydrogen bonds between peptide-water in method 1 was 16.221 while it changed to 14.340 in Method 2. Similarly, number of H-bonds between peptide-urea changed from 5.687 to 4.031 on switching from Method 1 to Method 2.
On checking radial distribution functions, interaction between water-peptide sites were somewhat similar for both Methods but significant changes were found for peptide-urea site-site correlations. Method-1 showed higher peptide-urea interaction.
What could be the reason for these discrepancies? Are both methods correct?
I want to go on with Method-2 for further simulations because it is relatively simpler but Method-1 shows higher hydrogen bonding between sites.
Please suggest.
yours sincerely,
Apramita
Relevant answer
Answer
Equilibration of pressure/temperature occurs quite rapidly, but full equilibration of conformational degrees can be extremely slow and usually cannot be achieved. Which is why people need to make further assumptions, use restraints, enhanced sampling methods etc.
  • asked a question related to Computational Biophysics
Question
3 answers
I am working in the field of protein chemistry.  Can anybody help me to do molecular dynamics and simulation.Is there any institute who can help me to do so????
Relevant answer
Answer
These tutorials could help you to the best. As you mean that, you are beginner, start with Tutorial 1: Lysozyme in Water
BUT, if you are already familiar with MatLab, you can checkout http://www.ergodic.org.uk/MDdotM/MDdotM.php?About&headerbar=1
  • asked a question related to Computational Biophysics
Question
1 answer
Hi
I would like to get he recent amber force field (topolgy-parameter) for performing MD simulations of RNAs containing modified residues. More importantly how to simulate system containing Guanine in Tautomeric form (force field)?
Relevant answer
Answer
You need to modify topology of your guanine residue to simulate tautomeric form. Exact procedure depends strongly on md software which you use.
  • asked a question related to Computational Biophysics
Question
3 answers
The H-bond graph between protein and ligand obtained after md is showing temporary bonds i.e. bonds are forming at certain frame and there is no bond at the rest of the trajectory. Please comment on this kind of ligand behavior. Also, is the interaction between ligand and protein is temporary in this case? What else can be done in order to assess the interactions after md.
Relevant answer
Answer
Dear Drista,
You should consider only those contacting residue pairs, which are found in more than 80% of the protein-ligand complexes in last 10 ns of the MD trajectories since they are more reliable to make stable interactions. Therefore, if you find hydrogen bond in a particular frame which subsequently vanishes down the trajectory, they might be some non specific interactions and are not stable contacts. 
1. In my opinion, you can improve by performing a rigorous docking experiment and set up a benchmark for further validation.
2. For trajectory analysis, you can specify two atoms which you think are interacting and plot their average distance throughout simulation and see if that converges or deviates a lot. For hydrogen bonding, you can set a theoretical range as cutoff distance and monitor how many frames these residues are fallin under this range.
3. For an overall quality monotoring, you can check the rmsd of the binding pocket and the ligand both in free and bound conditions and see if they significantly differ or not.
Best of luck!
  • asked a question related to Computational Biophysics
Question
3 answers
Hi,
I am new to GROMACS. I have a doubt. Suppose I have two groups in my system and I  want to restrain the Centre of mass of a particular group, then how to specify this in the refcoord-scaling=com option, where to specify center of mass of which particular group it will consider for restrain.
Please give suggestions.
Relevant answer
Answer
GROMACS does not have the ability to restrain a molecule based on its center of mass. The refcoord-scaling option determines how the origin of the harmonic position restraints is calculated, either scaled based on a relative (internal) coordinate calculated as the vector originating at the COM, or by each atom's position individually (refcoord-scaling=all). This is dealing only with how the reference positions are updated when pressure coupling is applied.
  • asked a question related to Computational Biophysics
Question
2 answers
Hello, everyone!
    Now I'm studying on the MD simulation of interface diffusion. After I got the trajectory of the atoms, I didn't find the solution to obtain the atoms' RMSD along the z direction(vertical to the interface). The software I used is VMD. I want to know if there're some skill to deal with the problem.
Thanks a lot
Relevant answer
Answer
When you use the formula for RMSD, instead of using the vector position r_i, use its projection along the direction you are interested (e.g., any direction n), so that in formula of rmsd, you replace r_i with
z_i = dot_product(r_i, n)
  • asked a question related to Computational Biophysics
Question
1 answer
what are the means and differences of "< |M|\S2\N >" , "< |M| >\S2\N" , "< |M|\S2\N > - < |M| >\S2\N" and "< |M| >\S2\N / < |M|\S2\N >" in .xvg file of g-dipoles command of gromacs?
Relevant answer
Answer
Hi Zaiddodine,
gmx dipoles -a calculates the average |M|2 plus its fluctuations. \S\N is a code used by xmgrace for superscripts, so X\S2\N means that the variable X is squared. 
  • asked a question related to Computational Biophysics
Question
3 answers
I want to perform the brownian dynamics of graphene oxide using Gromacs, but I don't know what to do. I have done many molecular dynamics simulation of graphene oxide and I am familiar with the  procedures. In brownian dynamics, do I need to build the model of graphene oxide?  Is perform brownian dynamics same as perform molecular dynamics? 
Relevant answer
Answer
You can use integrator bd as mentioned in the above reply, But when BD is used, it make sense to work with a more coarse-grained model than atomistic description.
  • asked a question related to Computational Biophysics
Question
4 answers
Hi,
I want to perform molecular dynamics simulation of protein-RNA complex at deifferent pH condition in gromacs. 
When I am using Amber force field, It is not detecting protonated residues while OPLSaa force field is not detecting nucleotides. 
Is there any other software available to perform this simulation??
Relevant answer
Answer
Hi, Karolina.
I want to perform the simulation of protein-RNA complexes at different-2 pH conditions. 
I used OPLSaa force field to do that for protein alone, but when I am doing that for protein-RNA complexes, it is showing errors.
Amber94 is asking me to delete all extra hydrogen atoms, which I have added during protonation of protein wherever OPLSaa is not detecting nucleotides. 
 So, How can I  do that without modifying force field? 
  • asked a question related to Computational Biophysics
Question
7 answers
 I am using this command in cpptraj
rms ToFirst :1-81&!@CA,C,N,O*= first out rmsd1.agr mass
Plot is generate using  number of frames.How to plot rmsd of amber trajectories in time unit  ns using cpptraj ?
Relevant answer
Answer
Hi,
you could try the "time" keyword in rms command.
I don't know how many frames there are in your trajectory, but assuming you are saving your coordinates after each 1 ps, you could try typing:
rms ToFirst :1-81&!@CA,C,N,O*= first out rmsd1.agr time 0.001 mass
Hope that helped.
Karolina
  • asked a question related to Computational Biophysics
Question
5 answers
Hi,
I'm doing MD simulation using Amber. Every time when I measure the RMSF and RMSF it is always very high. I don't know what is the problem. THe RMSD remains stable but get high as 6 to 10 Angstrom. is this a problem or not. I also extend my simulation but no fruitful results till now.
I have also attached an RMSD plot for reference. 
Relevant answer
Answer
Hi
First share the protein resolution and are you taking the structure from PDB?
As you mentioned your structure contain half of loop and if it's a crystal structure with good resolution, then no need to go for loop refinement. But if you are modelling the protein by homology or ab-initio then you must have to do loop refinement. You can't find anything worthy within 5ns simulation. So my suggestion is do a long equilibration and do production for long time scale (minimum 50ns) for some worthy results. 
  • asked a question related to Computational Biophysics
Question
2 answers
Is polarizable MARTINI models compatible with atomistic models of protein (hybrid simulation) in NAMD? what considerations should I take for timestep in these cases? I'd appreciate your suggestions and comments with references to topo and par files. Is there a better or coarser model for water that can be used in NAMD? The simulation is aimed at docking analysis.
Relevant answer
Answer
@Abdallah: Looks like a good tool, though it needs a modified version of NAMD. I will try it out anyway.
  • asked a question related to Computational Biophysics
Question
8 answers
Hi guys, I am an undergrad who just started working on molecular simulations. Currently I have to do a molecular simulation with adenosine deaminase and guanine deaminase. PDB file of adenosine deaminase shows it contains a selenomethionine and pdb of guanine deaminase shows it contain a xanthosine. Those two residues cannot be recognized by amber or charms forcefields. What will be the best tool for me to create forcefield files for those two residues?
Relevant answer
Answer
I hope the protocol from this research paper might help you.
"To prepare the system, we replaced the selenomethionine used for crystallisation with methionine, then we ran an MD simulation first on the apo protein for 15 ns. Then, we used the structure from the last frame of the previous simulation as a starting point, inserted ATP + Mg2+ into the molecule, and ran a simulation for 30 ns."
  • asked a question related to Computational Biophysics
Question
2 answers
Hello everyone
I want to simulate a small organic molecule in which Iodine atom is linked to Carbon of benzene ring. I am using GROMOS54A7 force field and obtained atom types and charges etc. from ATB server. I am curious about the parameters for Iodine atom. Can I replace the atom name of I with C? Keeping the charges and weight of Iodine intact. And how to obtain the bonded and non-bonded interactions
Relevant answer
Answer
The nonbonded parameters for I and C will be wildly different so renaming is not advisable, since ATB will then be confused as to what it's trying to do. Most conventional force fields do not treat halogens correctly, as they do not model the sigma hole that gives rise to halogen bonding. We recently published parameters for halogens that include this effect: http://dx.doi.org/10.1016/j.bmc.2016.06.034 
I think our parameters will deal with halogenated species better than any GROMOS parameter set.
  • asked a question related to Computational Biophysics
Question
10 answers
Can someone suggest what "Molecular Dynamic simulation" is and how to study it? 
  • asked a question related to Computational Biophysics
Question
2 answers
Hello,
I performed 20ns simulation of a protein using Gromacs 5.1. I want to plot  DSSP plot of simulated protein for specific residues. I created index file using following command. 
gmx make_ndx -f f.gro -o A.ndx
But when i used the above ndx file in DSSP command. I dont see desired residues secondary structure plot.
Can anybody please let me know how to do it.
Thanks,
Sai
Relevant answer
Answer
You can use the script file at following link to fetch information from .xpm file generated by gmx do_dssp. Using thst you will get residue vise sec. st. components which you can plot for your desired range of residues:
Thanx to Bevan lab :)
  • asked a question related to Computational Biophysics
Question
5 answers
I am a little confused by the unit cell dimensions of the entry:
When I download the .pdb file there is only one molecule of protein with water accompanied by a unit cell dimension capable of fitting 4 molecules (this is viewed in the 3DView of PDB website as BioAssembly1). When I go to the link above and view in 3D, select "Unit Cell", it shows me 4 molecules of protein with water. 
I was hoping to find a way of downloading the 4 molecules to pack the unit cell, but I can't seem to find a way. Is there any way of recreating the packed unit cell in Gromacs i.e., replicated the protein molecule to create the 4 proteins in the correct position. 
Relevant answer
Answer
Also note that this kind of construction is very simple to do in CHARMM (or online via CHARMM-GUI).
  • asked a question related to Computational Biophysics
Question
6 answers
Can someone suggest what "Molecular Dynamic simulation" is and how to study it? 
Relevant answer
Answer
  • asked a question related to Computational Biophysics
Question
3 answers
hello,
A protein which is composed of dimer of heteromers (αβγ). I want to simulate this protein to study the correlation between structure and function. what you will suggest for simulation to take the monomer form or in the form of dimer? is the monomer form simulation will represent their natural dimmer form?
Relevant answer
Answer
Mr. Nasir,
The computations of monomers cannot reproduce the energetics of dimeric protein interacting ensembles. 
  • asked a question related to Computational Biophysics
Question
5 answers
Schrödinger software
for a beginer
Relevant answer
Answer
Hi som
It depends on 2 parameters;
First and most important being the hardware of your system. Better graphics card, , memory and processor is an advantage.
and Secondly it depends on the time(ns) you have put the simulation for.
Generally,with medium range hardware and simulation for 60 (ns) it  may take around 2-3 days.
I hope it helps.
  • asked a question related to Computational Biophysics
Question
4 answers
Do I need to minimize my ligand using sander if I just wanna do standard molecular docking using AutoDock, not molecular dynamics? Do I have to stop until adding AM1-BCC charges by antechamber?
If no, what are the steps needed for ligand minimization after drawing it on MarvinSketch. Thank you.
  • asked a question related to Computational Biophysics
Question
6 answers
Hello everyone,
Actually I faced a problem regarding movie making and analysis after simulation from multiple DCD file on NAMD.
So, actually I want to run 1000000 steps of steered molecular dynamics of a large protein containing 546445 atoms. so it was very much time consuming job. so i want to carry out the job using multiple restart file on NAMD.
But i don't know how to make the movie and final analysis of  the steered molecular dynamics job from multiple DCD file and Restart file.
So, can anyone help me to find out the solution.
Thanks in advance.
Relevant answer
Answer
If you want to concatenate dcd, you have the catdcd tool in vmd:
Once you have your desired .dcd file, with the desired timestep, you can use the typical way to do a movie of a trajectory:
  • asked a question related to Computational Biophysics
Question
4 answers
Hi everyone, I am using gromacs 5.1 for COM pulling of the ligand from a lignad-protein complex. I am getting an abrupt fluctuation in the position of the ligand near 110ns and 270 ns (as you can see in the attached figure) which should not be there. So my question is, What is the possible reason that leads to fluctuation and how it can be fixed?
Relevant answer
Answer
Why shouldn't those increases be there? Nothing seems abnormal to me. Watch the trajectory and see what is happening on those frames. Probably a side chain is flipping out of the way or something, allowing for a quicker movement of the ligand.
  • asked a question related to Computational Biophysics
Question
2 answers
I am trying to set up a molecular dynamics (GROMACS) simulation to study the effect of crowding agent on protein structure. I have referred several literature papers where they have mentioned modelling the crowding agent as a hard-core sphere but couldn't find relevant information to include spheres in the solvent. Can somebody please explain how to model and incorporate hard core spheres into the box along with the solvent and protein? Kindly let me know if any materials are available related to this work.
Relevant answer
Answer
You can use tabulated potential. You can find the format for the tables in the manual
  • asked a question related to Computational Biophysics
Question
6 answers
I am doing all-atom MD simulations. I want to simulate a complex system containing DNA and protein. I found papers, where most people have used AMBER force field for DNA/RNA systems. Earlier, I have done simulations with CHARMM36 forcefield for only protein system. I would like to know, whether should I continue with CHARMM, which also has the definitions for nucleotides or switch to AMBER forcefield for DNA-Protein complex and why?  
I would also like to know that what parameters in *.mdp change on changing molecule type (only protein to DNA/protein-DNA complex) and/or forcefields.
Relevant answer
Answer
Amber has good nucleic acid-specific force field corrections, especially those based on developments by the Orozco group (parmbsc0 in 2007, parmbsc0/OL15 in 2015, parmbsc1 in 2016), and most protein-DNA papers I see refer to this particular sets of parameters - it has become a standard to some degree, in the same way that CHARMM is preferred for lipid and perhaps protein simulations. So while it might not be perfectly obvious that one particular FF is in every regard better than the other, there seems to be a clear field-specific preference in terms of usage. Look up the linked paper for a more in-depth discussion.
In terms of .mdp settings, I don't think you need to make any significant changes to the simulation protocol when adding DNA to your system.
  • asked a question related to Computational Biophysics
Question
2 answers
I am working on nucleic acid (NA). I have to add K(+) ions to study its behaviour. I want to keep the coordinates of NA molecule and K(+) fixed & allow water molecules to equilibrate. This step is necessary to prevent the fast diffusion of bare K(+) ions, unprotected by their solvation shells, towards NA. I want to carry out the following steps. 1) NA and K(+) fixed, water molecules are allowed to move (equilibrate) 2) NA fixed, K(+) and water equilibration 3) All three are free to move. I have generated the position restrain file (*.itp format) for K(+) by using .ndx file & genrestr command. My question is where and, how do I need to plug .itp file in topol.top.
Format of position restrain for K(+) is :
[ position_restraints ] ;
i funct fcx fcy fcz
141985 1 1000 1000 1000
141986 1 1000 1000 1000 : : here 141985 is the atom index of the first K(+) ion and so on.
Relevant answer
Answer
 @Dries Van Rompaey,
I figured it out a couple of days ago. Will ask specific question on gmx-mailing_lists from now onwards !!
Thanks for your inputs & concern.
  • asked a question related to Computational Biophysics
Question
7 answers
I am simulating a single chain with AMBER force field. After energy minimization, I got a force less than 10 kJ/mol/nm, but energy converged to a positive value. Does it mean my simulation was wrong or something else?
Thanks in advance.
Jing
Relevant answer
Answer
The energy is negative if the favorable nonbonded interactions dominate over unfavorable interactions and bonded terms. The bonded terms are, by definition, always positive. In vacuo, you have no solvent, which is what dominates the favorable interactions in solution. So this is what happens; the bonded terms dominate the total potential of the system.
  • asked a question related to Computational Biophysics