[gmx-users] Pressure Coupling Problem

[chris.neale at utoronto.ca]

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.neale at 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 ...