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Questions related to Gromacs
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 5,116 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 4,109 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 431 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 7,566 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 9,115 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 4,598 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 4,408 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 3,126 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 1,659 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 10,081 2 View
Hi everyone, I need to buy a new laptop. I do the first steps of molecular dynamics by GROMACS (on Ubuntu) with my laptop, but I don't need to do equilibration or final MD run here, I do them on...
29 September 2020 9,665 4 View
I performed in-silico acetylation using PyTM plugin but there are certain clashes that I want to resolve. I couldn't perform energy minimization using gromacs, chimera as they do not have default...
27 September 2020 3,956 6 View
My system consists of ionic liquids, aliphatic and aromatic hydrocarbons. Any suggestions and any script for calculation of viscosity?
25 September 2020 6,685 1 View
I was trying to apply restraints on my molecules, however, they were still moving after I put 100000kJ/mol/nm^2 on them. I am sure my topology is correct, so I think maybe its the correlation of...
24 September 2020 4,161 3 View
I am using Ubuntu 20.04 and I have PyMol installed, with a license. But it has been impossible to add the repository ppa:makson96/dynamics. Even downloaded from github, the package with the...
21 September 2020 7,022 1 View
Hello everybody I use gromacs software but I do not know what code to use to get the number of water molecules in the carbon nanotube. If anyone can help Please Thanks a lot🙏
13 September 2020 1,077 6 View
Hello Everyone, I am using gromacs for MD simulation of the protein-ligand complex. I am using CHARMM force field but it is continuously showing the following error. I checked and some people...
10 September 2020 2,198 3 View
Dear all, I am looking for a way to restrain the center of mass (COM) of two different molecules bathed in water, using GROMACS 2018. The only thing close I found on gromacs that does this is the...
08 September 2020 4,891 8 View
Dear all, I have done simulation of two carbohydrate molecules in Gromacs with simulation box length of 6 nm. I have corrected the trajectory using trjconv with pbc mol and center flag as used in...
05 September 2020 391 5 View
Hello, I've used GROMACS to perform a short REMD simulation (200 ps) in order to test whether my choice of temperature range allowed sufficient exchanges between replicas. The REMD simulations...
03 September 2020 9,464 3 View
I'm using Gromacs 2020.3 for molecular dynamics calculations using an AMD Rx 580 GPU. However, analyzing the log files I realized that in fact the Intel GPU of the CPU itself is being used and not...
29 August 2020 3,608 1 View
Hi :D I'm using Gromacs 5.1.5 for MD simulation. For binding energy calculation, I used g_mmpbsa (version 5.1.2) I simulated the protein for 150ns and nojump of my xtc file. Then cut last 50ns for...
26 August 2020 7,687 1 View
Hi everyone, I am new gromacs user. I am doing the MD simulation of protein-NA. I did the Energy minimization step, NVT, NPT equilibration. after equilibrating the system i submitted the...
22 August 2020 8,008 4 View
I chose C-alpha as a group for root mean square calculation(rmsf), but why my rmsf calculation in gromacs did still count on atom-based, not residue-based? The command I used: gmx rmsf -f...
18 August 2020 1,477 6 View