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Questions related to Gromacs
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 1,964 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 5,736 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 8,591 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 8,966 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 2,754 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 8,672 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 9,035 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 638 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 9,421 3 View
I have a question regarding Gromacs. I want to know whether Gromacs can calculate the interaction of each OH group of the sugar rings separately in bilayer or it just shows the number of whole HB...
27 August 2021 8,225 2 View
Hi all, Does gromacs have any option for adding external forces and torques to the atoms? the ones that change by the time and atom properties. like the fix add force and add torque command in...
26 August 2021 5,576 1 View
I've run a simulation for an apoprotein using fourierspacing = 0.16, and I want to run a protein-ligand complex simulation (all using Amber ff). I found that it's suggested to set the value of...
25 August 2021 1,661 5 View
I'm using Gromacs 2020 to run a protein ligand simulation using Amber99SB for protein and Amber (GAFF) for ligand, in the mdp files should rlist be of the same number as rcoulomb and rvdw e.g....
24 August 2021 5,761 2 View
I want to look at all my alanines in my protein chain and want a selection in VMD just for this. I don't know what their resID numbers are but want to be able to select them all by the fact they...
24 August 2021 5,481 1 View
Hi. I am running transmembrane protein simulation. I am confused at position restraining. During the shrinking steps using inflategro.pl script, tutorial mentions experimental value 0.69A but i do...
19 August 2021 5,967 5 View
It is known that in order to quantify chaos in a dynamic system, the maximum Lyapunov exponent must be detected, but before applying Lyapunov detection, is there any way to know at a glance a...
16 August 2021 5,456 3 View
Hello everyone, I want to use g_mmpbsa for interaction energy analysis Can anyone tell me about how can I install g_mmpbsa in gromacs 2020. Also, can anyone suggest me about which are the other...
07 August 2021 5,857 10 View
I've seen in some articles talked about parameterizing ions force field, for example here Effect of Ca2+ on the promiscuous target-protein binding of calmodulin the authors talked about...
05 August 2021 7,030 1 View
Is there any step-by-step protocol/procedure for the membrane protein (bilayer) ligand Gromacs Simulation? I could able to obtain a bilayer with the protein incorporated from the CHARMM GUI...
02 August 2021 7,282 2 View
I could able to obtain a bilayer with the protein incorporated from CHARM GUI sever, Now I am stuck; how to insert ligand on the system. I am looking forward to a useful site or protocol for this...
02 August 2021 1,500 0 View
How to use gromacs to build topology after peptide C-terminal amidation ？
31 July 2021 182 2 View
Hi, I would like to calculate the SASA of a protein structure. Along with the total SASA, it would be interesting to see the hydrophobic and hydrophilic surface area. I know there is a tool...
21 July 2021 6,798 5 View
Hello everybody, I am trying to download the top2psf.pl script from the VMD script library (https://www.ks.uiuc.edu/Research/vmd/script_library/scripts/top2psf/) but I am getting an error from...
20 July 2021 4,908 3 View
Hello all, I am new to MD and GROMACS. I was faced with the task of calculating the surface tension. As far as I know, the calculation parameters in *.mdp file, such as rvdw, rcoulomb, etc....
16 July 2021 3,377 3 View