[gmx-users] Pressure Coupling Problem
ilchorny at gmail.com
Fri Apr 10 19:12:07 CEST 2009
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.
On Fri, Apr 10, 2009 at 8:05 AM, <chris.neale at 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.
> -- 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
> 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
> [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
> 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?
> -- 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
> large proteins, at least from my experience. I have since run 400 ps NVT
> as ...
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