[gmx-users] Pressure Coupling Problem

Joe Joe ilchorny at gmail.com
Fri Apr 10 06:44:42 CEST 2009

Nope not an A/nm problem.
As a simple test I take spc.gro from share/top.
I reconfigure the box (i.e. editconf -f spc.gro -d 1.0 -c -bt cubic -o

I then solvate with genbox, minimize and run using the mdp file I provided

No matter how much minimization I do the volume of the box expands when run
it using berendsen pressure coupling with a tau_p -f .1.


On Thu, Apr 9, 2009 at 11:22 AM, Chris Neale <chris.neale at utoronto.ca>wrote:

> 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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