From: genie lfs (lfs.use_at_gmail.com)
Date: Wed May 10 2006 - 04:48:44 CDT
i am trying to do rna-protien interactions. upon following references
choose to use PBC and PME opitions for the simulation in a NPT
i am using the configuration parameters as attached . i am using
different configuration files for the equilbration and productive
phase and using shell script run the simulation. the simulation
crashes when running the fourth.namd complainng " FATAL ERROR :
periodic cell has become too small for the original patch grid "
am i doing anything wrong in the simualtion?
and also the simulation runs very slowly compared to non PBC , non- PME .
my system has 8.440 atoms (including water) and running on 7 cpus . it
still take s 3-4 days for the simulation.
any help would be appreciated greatly.
and hoping a reply
ps: i had to restart the simulation in between also..
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