Re: Error while running NPT Simulation

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu Oct 16 2008 - 13:27:24 CDT

On Thu, 16 Oct 2008, Nd S wrote:

NS> Hi all
NS>
NS> I ran a NPT simulation and the volume of the cell decreased from
NS> 1,001,290.4628 to 471,602.1941 and after that the simulation crashed giving
NS> the following error:
NS>
NS> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 65000
NS> WRITING COORDINATES TO DCD FILE AT STEP 65000
NS> WRITING COORDINATES TO RESTART FILE AT STEP 65000
NS> FINISHED WRITING RESTART COORDINATES
NS> WRITING VELOCITIES TO RESTART FILE AT STEP 65000
NS> FINISHED WRITING RESTART VELOCITIES
NS> FATAL ERROR: Periodic cell has become too small for original patch grid!
NS> Possible solutions are to restart from a recent checkpoint,
NS> increase margin, or disable useFlexibleCell for liquid simulation.
NS>
NS> I ran the simulation for 100,000 steps. The unit cells contains only a
NS> derivative of 1-Hexene. Can you please explain me what happened and how I
NS> can correct this.

as the message says, your cell has shrunken a lot. too much for
the parallelization strategy of NAMD. ...and as the message says,
you can just continue from the last restart and go on.

now, whether the shrinking is the proper behavior, only you
can tell. e.g. by comparing the density to what you would expect.
if it is far too high, then it would be an indication that (some of)
your potential parameters are crap.

axel.

NS>
NS> Thanks a lot,
NS> Navdeep
NS>

-- 
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Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
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