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Questions related to Gromacs
I want to analyze the responses and conformational states of proteins at various temperatures in silico. Can I do this with molecular dynamics simulation programs like gromacs? Is there a special...
11 December 2021 7,566 3 View
Fatal error: Syntax error - File CHL.itp, line 7 Last line read:'[ atomtypes ] ' Invalid order for directive atomtypes. During the energy minimization step, I've obtained this error when I'm...
08 December 2021 1,612 3 View
Dear all I have few confusions about the pulling code in gromacs, I was using NAMD before and the method was quite straighforward in NAMD to pull the ligand out of the protein, in gromacs it is...
07 December 2021 578 1 View
how to create the coordinate and topology file for cyclohexane? And will all atomic simulation be possible?
01 December 2021 4,492 4 View
Hi all, I have several sets of MD runs and I would like to perform PCA analysis using Amber. I am quite a newbie with this package being mostly used to Gromacs/NAMD. In particular I would need to...
24 November 2021 4,584 5 View
I've a gromacs trajectory of 500 ns whose size after removing the solvent is about 2 GB. I want to generate a movie highlighting certain residues, I tried Chimera, it crashed and couldn't even...
21 November 2021 7,745 6 View
Dear all, I am doing simulation for a polymer/water system. I would like to do RDF and coordination number analysis for this system. I got results like in figure I attached here. I know the...
09 November 2021 9,200 3 View
Hello, I used gromacs 2020 and performed the 100ns simulation protein drug complex. I generated .tpr file for 100ns simulation using gromacs version 5 as g_mmpbsa works with gromacs 5x version...
02 November 2021 571 4 View
I am using Ubuntu 20.04 LTS on Windows 10. Problem is Ubuntu is not detecting any of my GPUs. I was working on Gromacs and when I tried to run simulations on GPU it said GPU not detected. Gromacs...
28 October 2021 7,387 4 View
I want to see the conductance of ions by computational electrophysiology. How can I do it in gromacs 2020
25 October 2021 2,778 2 View
hello I want to make 2-dimensional plot like a picture as I attached I do not know how I can make it by gmx rms command in gromacs. could anyone help me with this issue?
24 October 2021 9,431 2 View
I am extending a gromacs simulation from 100ns to 500ns, if I used a different -deffnm file name, will the generated trajectory file be complete and extended (i.e. 500ns) or will it be as if it's...
22 October 2021 506 3 View
Hi everyone, In the modeling protocol I am replicating, the authors do the following: "The TM is first parameterized with neutral termini using a cross-term energy correction map (CMAP)...
22 October 2021 6,994 2 View
I am trying to use vnc viewer to take control of a computer in another location to simulate a protein using Gromacs 5.4.1. In the first step of simulation I am using GROMOS96 54a7 force field and...
13 October 2021 2,626 6 View
I have a computer with one CPU (Intel Xeon Gold 6134 Octa-Core 3.20 GHz Processor) and GPU (Nvidia RTX 2070). I want to perform temperature replica exchange Molecular Dynamics on this machine,...
12 October 2021 7,886 5 View
After performing md simulation I want to see the atomic contacts between residues. For that I have performed gmx mdmat and followed by gmx xpm2ps by using following commands gmx mdmat -f...
10 October 2021 7,037 4 View
Hi, I'm using Gromacs 2020 for my simulations and I need to use some forcefield parameters published in the literature for calcite. The thing is that the paper I'm using gives force constants in...
08 October 2021 8,880 4 View
The IMPPAT database is a compilation of Indian medicinal plants. But there is not an option to download all phytochemicals together. Is there any way to download like that ?
25 September 2021 1,381 3 View
I want to analyze the interaction of an enzyme with small molecule of an FMN (flavin mononucleotide) but gromacs doesn't recognize FMN. It require for manual definition of FMN topology. Using...
24 September 2021 8,991 3 View
Hello All, I want to perform drug-membrane interaction studies using Gram-negative bacterial membranes. I used CHARMM-GUI to model asymmetric mixed membranes with Lipid A in the upper leaflet and...
24 September 2021 4,503 3 View
I am trying to reproduce a paper which has followed a simulated annealing procedure with a simultaneous decrease in harmonic force constant. a) Starts at 60 K, force constant = 5.0 x 104 kJ/(mol...
22 September 2021 4,724 5 View
I am performing validation study of designed protein (240 AA)through GROMACS. Ideally, pressure should be around 1 barr.However, I have received value of 3.47966 bar during my simulation run. what...
22 September 2021 8,695 3 View
I am looking for a decanol molecule (or similarly-sized alcohol) implemented in the CHARMM36 force field for Gromacs.
21 September 2021 7,372 2 View
Hi I have been trying to make a HMMM bilayer through CHARMM-GUI but since the protein of interest is a well spread one, with certain domains being intrinsically disordered, I had to make a box 20...
18 September 2021 4,929 2 View