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Questions related to Gromacs
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 5,095 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 9,302 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 2,728 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 2,052 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 7,479 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 2,238 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 9,200 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 4,545 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 5,041 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 8,006 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 492 1 View
Can anyone suggest me the proper way to perform MMPBSA using Gromacs ??
12 October 2020 5,515 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 1,144 4 View
Dear all Is it possible to calculate friction coefficient in Gromacs?
06 October 2020 2,738 2 View
I have studied the structural changes of a protein in 3 different concentrations of ionic liquids (50 mM, 500 mM, and 1M). On analysis of the RDF plots, I find that the magnitude of the RDF plot...
06 October 2020 5,360 2 View
Hey guys, the following command uses the -surf flag and it causes some unnormalized-looking g(r) (see attached png file): gmx_mpi rdf -s tpr.tpr -ref 'resname TST' -sel 'resname RER -f movie.xtc...
04 October 2020 4,322 2 View
Hi every body I want to simulate gas absorption with gromacs. I have a box with three part , amine and water in the middle of box and gas is around of it(gas+amine solution+gas). Firstly I...
03 October 2020 624 2 View
Dear researchers, I ran 250 ns MD simulation of estrogen receptor alpha-tamoxifen complex through Gromacs 2019 package using amber99sb-ildn.ff. Now, I am trying to calculate the binding energy...
03 October 2020 7,739 3 View
Hi. I'm analyzing a bilayer and I want to make an index for calculating tilt angle. my problem is I have no idea about how to create such an index which contains vectors in it. I would be...
02 October 2020 9,287 1 View
I would like to know if there is a tutorial for performing adsorption simulations of a material surface (graphite) and a protein.
01 October 2020 4,762 3 View
While running a simulation on any peptide or protein, is it possible for the secondary structures to change? For example, seeing a steady rise in helical content over the whole simulation?
01 October 2020 4,641 9 View
Dear all, I'm trying to employ replica-exchange with solute tempering 2 (REST2) in a system, but I have performance issues in the calculations. I'm using openmpi-3.0.0 and gromacs 2019.4 patched...
30 September 2020 3,349 1 View
Hi, I have done a protein-protein docking. Now I want to perform MD in gromacs. I am confused with forcefields. When I tried to findout, everywhere it is written for protein-ligand but I couldn't...
30 September 2020 1,906 3 View
Hello Researchers The support for g_mmpbsa is not extended for the latest versions of gromacs (2020). I have already performed 200ns simulations and wish to perform PBSA calculations. What could...
29 September 2020 10,472 2 View