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Questions related to Gromacs
I want to see the conductance of ions by computational electrophysiology. How can I do it in gromacs 2020
25 October 2021 2,719 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 9,347 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 399 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 6,915 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 2,537 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 7,821 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 6,941 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 8,797 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 1,285 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 8,911 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 4,421 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 4,650 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 8,615 3 View
I am looking for a decanol molecule (or similarly-sized alcohol) implemented in the CHARMM36 force field for Gromacs.
21 September 2021 7,242 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 4,825 2 View
I performed a 100ns run for several drug candidates, and i wanted to check their average binding energy using g_mmpbsa. the thing is that g_mmpbsa gave me a very high positive energy for a my...
18 September 2021 1,884 2 View
We have been working with a homodimer protein (Homology/Alternative) . A chain and a B chain are present. Two ligands bind to the protein at the same time. Should I use both chains (complete...
17 September 2021 5,660 2 View
I am currently working on silica slab preparation. For that I have generated the supercell in materials studio, but when I tried to export this into pdb, some unusual bond connectivities...
15 September 2021 8,539 2 View
I am installing gromacs with version is 4.6.5 report the error:cudaFuncSetCacheConfig failed: invalid device function. my cuda version is 10.0. how do i solve the problem?
15 September 2021 8,889 2 View
I am doing gromacs simulation. The gpu-util is not going above 52% and in certain cases above 30% as well. How to increase this gpu-util? I am using gromacs 2020.4 and ubuntu 2020.04
07 September 2021 2,660 2 View
Hello all, I want to simulate Gamma amino acids using GROMACS, if anybody know where to get the forcefield parameters for gamma amino acids , kindly direct me .. Thanks in advance.
04 September 2021 8,608 5 View
2 particles communicated to PME rank 3 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not...
31 August 2021 8,927 1 View
I am doing md simulation using gromacs. It showed that I have fatal error and according to the manual, the system is blowing up. However, Inhave increased the ns and decrease the fs but the...
30 August 2021 566 2 View
What is the best way of repeating simulations, say I have to run the 10 replicates of the same simulation trajectory which was previously simulated for 100 ns production run after minimization and...
30 August 2021 9,315 3 View