GROMACS version: 2023.3
GROMACS modification: Yes/No no
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I have a fundamental doubt regarding my equilibration methodology , for all my simulations , i always run NVT first and then NPT . I run NPT untill my avg pressure is near 1 bar. None of simulations failed during production or equilibration and no blow ups .On reading some discussions on this forum , i came to know that i have to also check potential energy , error estimate , also the total drift. Does this mean that all my simulations were incorrect and if i were to perform longer equilibrations they would give me different mmpbsa results or different conformations , etc . Also i wanted to ask if npt equilibration once with restraints and once without restraints is necessary. I usualy perform npt equilibration only with restraints, is it correct. Please help me in this regard
How much you need to equilibrate depends completely on how good you initial coordinates are, so it is difficult to give any general recommendation. But NPT equilibration with restraints is not useful, and might even be bad, as the pressure is not well defined when position restraints are present. You should run NPT equilibration without position restraints. Also, you can’t really run until the pressure is 1 bar, as the pressure fluctuates significantly. I would run 1-10 ns of NPT equilibration, depending on the system.
okay sir , thank you