GROMACS version: All versions
GROMACS modification: Yes/No
I want to ask a question about time steps. normaly gromacs use 2 fs time steps. Why 2 fs select as default? what will happen if we change it 3 fs?
GROMACS doesn’t normally use 2fs as a time step. The time step mostly depends on the force field adopted, e.g., you may run MARTINI simulations in GROMACS and use 20/30fs time steps. As far as I know, the value depends on the force field you use and not on the engine (GROMACS, NAMD, LAMMPS, etc., but technically it may depend on the integrator you use). Most all-atoms simulations (like with CHARMM force field) use 2fs, sometimes 3-4fs with mass repartitioning. This page can give you some hints about the integration time step.
Thanks for you answer @obZehn. So forexample if i directly change the 2fs to 2.8 fs you think the results will not be in good accuracy? And integrator can not predict correctly the bond angels and etc?
Ad hoc changes in time step without thorough evaluation of energy conservation and ability of the force field to reproduce known quantities is dangerous territory. Stick with standard methods, unless you want to take up a huge amount of time proving that your small change in time step is actually even worth it.
@jalemkul so if i want to change the fs what should i consider to change in mdp file? I just want to try and see the difference.
@ehsansyh Technically speaking, to change the integration time step you just have to change the dt value in the mdp file. However, JUSTIFYING, and thus proving, a change of integration time step is not trivial, as said by @jalemkul. You are clearly free to change whatever you want in the mdp file, but do not expect valid and sound scientific results in doing so. If you are in doubt, a literature search in the previous MD sims of systems like yours will most of the time clear any doubts about what parameters to use.
@obZehn Thank you for your response. I just want to try and see if it is possible to do new thing using AI. Make it faster in prediction.