[gmx-users] Pressure Coupling Problem

[Lucio Montero]

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.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.
  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 ...

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