VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Mar 06 2007 - 10:02:47 CST

Hi,
  Assuming this is a NAMD simulation, I'd suggest asking on the
NAMD-L mailing list as that's a more appropriate forum for detailed
simulation questions like this. The VMD-L mailing list has more than
enough traffic already, so let's try and keep it as on-topic if possible.
The general rule of thumb for posting on VMD-L is that at least some part
of the question should relate to VMD or the various scripts or plugins
that come with VMD or that people have written for themselves.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Mar 06, 2007 at 01:37:47PM +0100, Rita Cassia wrote:
> Dear All,
>
> after creating an ethanol box, I had done simulations from 0K to 150K (2 ps), then another one, heating until 300K (NVT) for 60 ps. But I'm facing problems when I want to make a simulation (NPT) to equilibrate the density. The simulation stops , with the message
>
> "Periodic cell has become too small for original patch grid; Possible solutions are to restart from a recent checkpoint,
> increase margin, or disable useFlexibleCell for liquid simulation."
>
> I would appreciate if someone can give me some tips.
>
> Thanks in advance
>
> Rita Leite
>
> AG Photobiophysik
> Inst fuer Physik - HU Berlin
>
>
>
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-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078