Alright, sorry that I wasn't able to help. I'm confused by some
apparent contradictions in your posts and I'm not sure that I'm going
to be useful to you here.
Quoting
http://www.gromacs.org/pipermail/gmx-users/2009-April/041173.html: "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."
Quoting
http://www.gromacs.org/pipermail/gmx-users/2009-April/041159.html: "So
I got my small water box (800 waters) to behave stably with pressure
coupling after more minimization ..."
Good luck.
Chris.
-- original message --
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
water_center.
I then solvate with genbox, minimize and run using the mdp file I provided
earlier.
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.
Ilya
On Thu, Apr 9, 2009 at 11:22 AM, Chris Neale <chris.ne...@utoronto.ca>wrote:
[Hide Quoted Text]
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 ...
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