From: CHINDEA Vlad (vchindea_at_hotmail.com)
Date: Thu Nov 06 2008 - 17:40:35 CST
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 ?
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