I don't know the conditions you use with your system, but sometimes there are
problems when you use pressure coupling in a system with positionally
restrained or fixed atoms.
Cheers.
Lucio.
From: Joe Joe
Sent: Friday, April 10, 2009 12:12 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Pressure Coupling Problem
I finally figured it out. I went through every parameter step by step and it
turns our I had epsilon-r set to 80. Not sure why I had that. Wish gromacs
would have given me a warning (hint hint). That explains why my P.E. was 10^-5
instead of 10^-6. Thanks everyone for trying!!!. Sometime the most obvious
mistake takes some time to figure out.
Cheers,
Ilya
On Fri, Apr 10, 2009 at 8:05 AM, <chris.ne...@utoronto.ca> wrote:
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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