GROMACS version:2021.4 Hi, I am a beginner in Gromacs, now I have a basic question about the protein simulation in vacuum. Q; I want to simulate the protein in vacuum and water condition respectively to test the effects of water to protein. The protein can be obtained from PDB, (xRay method), and it has 14 negative charges. what should I do to modify the protein before I pu…

GROMACS version:2020.6 GROMACS modification: No When I do MD simulation about DES extraction citral, the volume of the box becomes huge after a period of time.And before MD simulation, NVT and NPT has been finished normally, so anyone can tell how to solve this problem? here is my md.mdp： define = integrator = md dt = 0.001 ; ps nsteps = 100000000 ; 200ns comm…

GROMACS version: GROMACS modification: Yes/No Here post your question Hi all, I’m simulating a protein with two chains (A + B). Each chain has a ligand bound to it. Both ligands are identical. I was following the protein-ligand tutorial on gromacs. When I visualise my processed complex file (complex.gro), I can see both ligand are overlapping rather than bound to their respecti…

GROMACS version: 2022 GROMACS modification: No I’m trying to calculate potential energies from an .xtc file and the original .tpr file. Since I don’t have an .edr file, I’m doing gmx mdrun -rerun. The .xtc file has ~500 snapshots that are spaced 1ns apart. With these files, when I do the rerun, it says I get the following warning: WARNING: This run will generate roughly 34113711…