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

From: Dave Rogers (wantye_at_gmail.com)
Date: Fri Nov 07 2008 - 12:23:52 CST

But it would be nice if someone threw in a function call to
reinitialize the patch grid instead of breaking when this happens...

~ David Rogers

On Fri, Nov 7, 2008 at 12:31 PM, Joshua Adelman <jadelman_at_berkeley.edu> wrote:
> 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
>>
>>
>> _________________________________________________________________
>> Connect to the next generation of MSN Messenger
>>
>> http://imagine-msn.com/messenger/launch80/default.aspx?locale=en-us&source=wlmailtagline
>>
>
> ------------------------------------------------------------------------------------------------------
> 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
> ------------------------------------------------------------------------------------------------------
>
>
>
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:50:04 CST