Hi all, I noticed that the mdp option “accelerate” is now marked as deprecated. Now, that approach never really instilled confidence, but are there any plans to implement anything more advanced, or do we stick with something like constant-force pull of the solvent or pull some sort of a solid piston introduced artificially? By something more advanced, here is what I mean: conside…

GROMACS version:2020.4 GROMACS modification: Yes/No Here post your question Good day, My slurm job tends to terminate and restart while mdrun is trying to write the *.gro file at the end, in HPC cluster. I could see from the *.err file that everything is fine until wait time is 0 s and my session hangs up and after sometime the job restarts. I think it’s an issue with mpirun…

GROMACS version: GROMACS modification: Yes/No Here post your question Good day! I am studying glutamic acid(E) to aspartic acid (D) mutations to look at its effect on a local lysine to form salt bridge. On comparing, one is effective in forming salt bridge ,but the other doesn’t and requires ions to counter. Is there any way to get ion accessibility to surface/residue? Thank y…

Dear All, Is it possible to increase the output precision of the gmx angle -type dihedral? Here are my commands: gmx angle -type dihedral -n index_file.ndx -f data_xtc_file.xtc -ov Dihedral.xvg For other properties, such as gmx trajconv, one can simply include the flag -ndec. This is not possible for gmx angle. I would like to avoid having to calculate the dihedral myself direct…

GROMACS version: 2021.2 GROMACS modification: No Hi there, I am very new to GROMACS and work with ab-initio calculations. It seems I need to compare the interaction energy obtained by DFT (Done with Psi4 and Turbomole) and LJ potentials by Force Field methods. The systems are small molecular dimers. Any help on how to do that in GROMACS? 1 post - 1 participant …

GROMACS version: 2021.2 GROMACS modification: Yes Added Amber14sb FF Hi, This is probably a naive question, but how can we run MD simulations with OPC water model with the Amber14sb FF ? Maybe is it better to stick with TIP4PEw or TIP5P water model for protein/ligand simulations. Thank you for your advices. Best Xavier 1 post - 1 participant Read fu…

GROMACS version: 2021.2 GROMACS modification: No Here post your question I have indexing issue in the xtc file format. my topol.to top file has the following items: ; Compound #mols IAUM 18642 protein XXXX; i have intentionally changed the Proteins to XXXX W 3798848 NA 1714 in the mdp file, I try to just output my NP, protein and …