So your problem with the small water box was solved simply by adding more
minimization? I then suspect that all of your problems are simply related to a
bad starting structure -- and by the sound of it is really is very bad. Are you
sure that you don't have an angstrom / nm problem here?
Chris.
-- original message --
So I got my small water box (800 waters) to behave stably with pressure
coupling after more minimization but I still can't get my large system to
work with pressure coupling. I tried minimizing but I can never get the Fmax
to be less 102, which is pretty normal for protein/water simulations of
large proteins, at least from my experience. I have since run 400 ps NVT as
the system (425K atoms) is quite stable. The <P.E.> is 2E-05. Since I am
using 4fs time steps gromacs won't let me use a tau_p less than .4. Not sure
what else to do except run NVT, which is what I was going to do after I got
the density equilibrated. BTW, I am using octahedral PBC, but that should
not make a difference with respect to P coupling, should it? Below is my
whole mdp file. As a reminder my density in the system goes from 1.0 - .1 in
10 ps with Pcoupl = Berendsen and Tau_p = .4. If I increase Tau_P then the
amount of time it takes for my system to expand increases but it still
expands.
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