Contact experts in Gromacs to get answers
1,323 views 1,449 posts
Questions related to Gromacs
I need to estimate the mobility of some atoms in the molecule within a molecular dynamics simulation and compare the values for different simulations. I use trjconv -fit rot+trans to fit C-alpha...
20 January 2021 661 3 View
The ligand.str file generated using cgenff is only compatible with charmm36. Any suggestions on how i can convert this str file into the gromacs topology file using Charmm27 ff?
08 January 2021 8,809 1 View
Hi, I got the following error message while running parallelized simulations with OpenMP: OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off...
03 January 2021 4,775 5 View
"Steepest Descents converged to machine precision in ,5780 steps but did not reach the requested Fmax
27 December 2020 1,467 3 View
Hello all, I want to do glycosaminoglycan (GAG) simulation in Gromacs. Initial structure and CHARMM topology for short chains can be obtained from Charmm GUI glycan modeler. But I have to take...
24 December 2020 6,265 2 View
Hello, I am using the one-step approach from https://rashmikumari.github.io/g_mmpbsa/single_protein_ligand_binding_energy.html to calculate binding energy between protein and ligand. However, I...
10 December 2020 7,385 1 View
Hi all. I have a query. It is about Whether GROMACS can do rmsd restraint of a protein throughout the whole simulation. I found Gromacs can do only position restraint. But my intention is the...
22 November 2020 597 4 View
I want to simulation cytochrome C that it has two parts HEME and protein. I have charmm files par_heme.pdf and top_heme.pdf heme group but I do not know how to convert pdf file to *. inp because...
14 November 2020 8,035 2 View
I tried to run a 500ns MD simulation of a protein in Gromacs. Due to power failure, my pc turned of after around 450+ ns. Now I want to restart the simulation from that point. I used the following...
14 November 2020 9,308 3 View
I am running MD simulations for holoenzyme in Gromacs. The protein has four chains like A, B, C, D. After MD simulations, All the chains are showing as X chain in VMD and even in the PDB file....
13 November 2020 6,349 1 View
I have done 100ns simulation using Gromacs. To calculate the RMSF, I used the following command- gmx rmsf -f md_noPBC.xtc -s md.tpr -o rmsf.xvg -res But when I plotted the graph in excel, I found...
13 November 2020 4,821 2 View
I'm currently running a protein simulation on GROMACS. I was originally using CHARMM22/CMAP for the simulation, but with some reasons I decided to switch to CHARMM36. The thing is, I expected...
11 November 2020 9,046 1 View
How can I calculate Hydrogen bond life time in Gromacs between two groups like water-water and water-specific group in a polymer?
11 November 2020 2,551 3 View
I am trying to use the gmx energy model to make free energy calculations upon binding of a ligand to a receptor. To do this I am invoking the energy module and adding the -odh flag: gmx energy -f...
10 November 2020 1,797 3 View
hi. I have done electrostatic potential analysis on a symmetric bilayer contains 10% Cholesterol but I've got this figure and I thought there is a problem with that as the potential is not...
10 November 2020 7,262 1 View
I have an enzyme, which has a small one turn alpha helix present on a loop surrounding the active site. I have to mutate one of the residues on the alpha helix with proline, so that it may be a...
04 November 2020 2,046 2 View
In order to calculate the MMPBSA, I am following the tutorial by rashmikumari (https://rashmikumari.github.io/g_mmpbsa/single_protein_ligand_binding_energy.html), but unfortunately, I am getting...
29 October 2020 9,005 3 View
Hi users, I found the topology files for choline with GAFF ff in literature (coa.ff and colinab3lyp08.prepi.txt) and I would like to convert these file to the input files I can use in Gromacs....
21 October 2020 4,379 3 View
Hello, I am trying to perform QM/MM simulations using Gromacs 2016.5, especially to model a transition state for a reaction. I found this tutorial that uses the Linear Transit approach :...
19 October 2020 4,871 3 View
I am facing a problem to make topology file using cgenff as instructed in Lemkul's Gromacs tutorial. But it didn't work as I couldn't get Networkx of version 1.11 . So, I am trying to find an...
19 October 2020 7,877 1 View
Dear All, I have to compute the enthalpy and free energy of a water molecules inside a complex system. I computed entropy using 2PT method but i need energy(potential or total) of the molecule to...
13 October 2020 337 1 View
Can anyone suggest me the proper way to perform MMPBSA using Gromacs ??
12 October 2020 5,304 3 View
Hello, After I minimized the protein structure I used editconf in gromacs to convert the minimized GRO file to PDB. when I visualized the PDB file produced, it was totally corrupted which...
10 October 2020 872 4 View
Dear all Is it possible to calculate friction coefficient in Gromacs?
06 October 2020 2,536 2 View