GROMACS version: 2020.1
GROMACS modification: No
OS: Ubuntu 20.4 emulator in Windows 10
EDIT: TIP3P shows the same problems
I am wondering if anybody has experienced problems running a conjugate gradient minimization of a TIP4P water box (7500 molecules, initial density 0.997). Steepest descent complains about waters not being settled during the first 200 steps or so (last warning step 226), but converges to machine precision in about 4000 steps (step size 0.01). Then, conjugated gradient crashes with the same error in about 600 steps (step size 0.0001).
Here’s what I tried:
I checked the structure output by the steepest descent minimization and didn’t find any bubbles, or anything that looked abnormal.
NVT simulations (annealing from 0 to 300K during 1 ns, then 300K for 1 ns) from the structure minimised by steepest descent run fine. Tried to minimise the structure output by NVT with CG and got the same error.
NPT simulations after NVT show big pressure fluctuations and end up crashing after a few ps (dt=0.0005, both with Berendsen and Parrinello-Rahman coupling)
This issue from a few years ago points out problems with TIP5P, but says specifically that TIP4P works perfectly. https://redmine.gromacs.org/issues/1348
So, I am wondering if that may be a problem with the linux emulator on windows that somebody has experienced before (I don’t have access to a linux machine at the moment), and if anybody has, did you manage to fix it?