Re: Charm++ Fatal error ! Periodic cell has become too small for original patch grid!

From: Joshua Adelman (jadelman_at_berkeley.edu)
Date: Fri Nov 07 2008 - 11:31:59 CST

Vlad,

There are a ton of discussions on this very matter scattered
throughout the namd-l archive. I would recommend going and reading
through the many informative responses to past inquiries of this type.

Josh

On Nov 6, 2008, at 3:40 PM, CHINDEA Vlad wrote:

>
> Hello everybody
>
> I am trying to simulate a small mollecule in a box of water both as
> a learning exercise and as a step in understanding a larger system.
> The box is 18 x 16 x 16 A and the molecule is about 4 A large, and I
> am using a configuration file derived from the ubiquitin tutorial.
> 1-2 seconds after the simulation is started I got the following
> error message:
>
> 'Charm++ 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.'
>
> What is 'The patch grid' refered in this message ? It couldn't
> possible be the PME grid since I have disabled this option.
> Obviousely there is no recent checkpoint to restart from, I am not
> sure what margin I should increase and useFlexibleCell was allready
> disabled.
>
> An xst file is generated before aborting with the following content
> (initial box size and center):
>
> # NAMD extended system trajectory file
> #$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z s_x
> s_y s_z s_u s_v s_w
> 0 15.931 0 0 0 18.638 0 0 0 15.349 1.2226 -1.0244 -0.6799 0 0 0 0 0 0
>
> Any ideas on what could be wrong ?
>
> kind regards
> Vlad
>
>
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------------------------------------------------------------------------------------------------------
Joshua L. Adelman
Biophysics Graduate Group Lab: 510.643.2159
218 Wellman Hall Fax: 510.642.7428
University of California, Berkeley http://nature.berkeley.edu/~jadelman
Berkeley, CA 94720 USA jadelman_at_berkeley.edu
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