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Questions related to Gromacs
I want to calculate Orientational tetrahedral order parameter of water. The output of gmx_hydorder is confusing. can I use gmx_order instead?
18 January 2020 6,737 4 View
Hello everyone, I am running a simulation for 500 ns but after 200 ns I get the following error: The input requested 100000000 steps, however the checkpoint file has already reached step...
17 January 2020 548 7 View
Hi all, Could someone tell me how to calculate the electrostatic potential across the z axis of a lipid bilayer ? Also, I would like to calculate the potential from the lipid headgroup to a...
05 January 2020 3,375 9 View
I've a new ligand and named it as 'UNK' in pdb file. While generating the ligand topology through GROMACS by following its protein-ligand tutorial. I'm getting this fatal error: " Residue 'UNK'...
02 January 2020 5,593 10 View
Dear researchers I am facing this error during the free energy calculation of protein-ligand for which I have applied restrained to some atoms of protein residue and ligand. A list of missing...
01 January 2020 5,255 4 View
HI All, "ERROR : No.of Coordinates in Solv.gro and Topol.top not matching" I am trying to run GROMACS simulation for Protein-Ligand complex, and I am facing this issue, and I dont know how to...
01 January 2020 9,041 3 View
While running mdrun_mpi, I am getting following error. I have intel compiler 2018 in the cluster. And used openmpi 4.0.1 for gromacs mpi installation. Abort(1094543) on node 0 (rank 0 in comm 0):...
01 January 2020 6,959 9 View
Good day, I have downloaded the latest version of DSSP from the site : https://swift.cmbi.umcn.nl/gv/dssp/ however as I downloaded and extract the package I see it is named hssp 1.3.4 and the...
01 January 2020 3,695 1 View
01 January 2020 4,005 4 View
Hello everyone, I'm running MMPBSA by using the g_mmpbsa tool for GROMACS. However, it runs extremely slow even though it's claimed that by default it uses all the processors:...
01 January 2020 2,549 1 View
Hi. I want to do simulate via gromacs for ligand- protein complex which there is 9 ligands (three of them are seperated and six of them are connected together(picture in Add files). when I used...
01 January 2020 7,841 5 View
I am performing protein ligand simulations in Gromacs. In md simulations how can one fix these dangling movements of residues near protein terminals? I think this will interfere in my RMSD or...
01 January 2020 9,945 3 View
Dear all, I have a question regarding loading .xtc file (with no periodic boundary conditions) to VMD which I generated before. To this end, I had used the command: trjconv -f md_0_10.xtc -s...
01 January 2020 1,046 4 View
Hi, I'm up against a horrible deadline so I'm hoping for some help figuring out what I'm doing wrong. I have a list of custom atom names in Gromacs of which I want to perform hydrogen bond...
01 January 2020 8,495 5 View
I have generated parameters for Doxorubicin using ATB server to be used with gromacs. I have calculated solvation free energy of doxorubicin (parameters generated by ATB) which gives a value...
01 January 2020 6,154 3 View
i have simulated a system consisting of water, cation and an anion, now i want to get individual energy profile for them can anybody help me regarding that. i have used the gmx energy command but...
01 January 2020 5,351 4 View
01 January 2020 9,414 10 View
Can anyone give me a rough estimate of time it takes for ATB (gromacs)server to give the parameters for the submitted molecule ?
01 January 2020 4,510 3 View
There is a model of thylakoid membrane in water with a given ratio of lipids (360 lipids in total). And i'm trying to do the right simulation in GROMACS. For this i need to know the surface...
01 January 2020 5,798 2 View
01 January 2020 727 3 View
I am trying to do PCA from the MD trajectory of a multi-domain protein using GROMACS tools. I am using gmx covar and gmx anaeig for PCA. My protein has many domains, but I would like to focus on...
25 December 2019 3,928 4 View
I have tried to run simulation for protein complex of NRAS(5UHV) bound with Mg and GTP. However I have encountered the following error while using pdb2gmx: Program pdb2gmx, VERSION...
19 December 2019 2,335 3 View
Hi. I am using gromose 54a7 force-field and Gromacs package to simulate a protein-ligand complex.it writes pdbs for steps. Maximum force = 8.3529562e+04 But in the NVT equilibration step, the...
17 December 2019 8,488 2 View
12 December 2019 7,280 2 View