Re: gpu pressure control

From: Chris Harrison (
Date: Sun Jan 04 2009 - 12:23:48 CST

JC's right, this sounds *very* much like a diff in the decomposition of the
system into patches; particularly since NPT runs ok but (presumably) NVT

However .... since NPT vs. non-NPT (presumably NVT) apparently differ this
implies your system may only be equilibrated within the NPT ensemble and not
well equilibrated overall. This may or may not matter depending on the
property you are interested in evaluating from the simulation data.


Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 Voice: 217-244-1733 Fax: 217-244-6078

On Sun, Dec 28, 2008 at 11:10 PM, Daniel Miscevski <> wrote:

> Hi all,
> While running a test with the gpu enabled version of namd, I get and error:
> Reason: FATAL ERROR: 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.
> But if disable the constant pressure control, it runs fine!
> When I run the same test but on the cpu only version of namd with the
> constant pressure control enabled, it runs fine.
> Any ideas?
> Thanks,
> Daniel


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