[gmx-users] protein unstable for parallel job while stable for serial one

Akansha Saxena asaxena17 at yahoo.com
Mon Sep 18 17:21:46 CEST 2006


Has anybody seen a protein becoming unstable on
parallel nodes while remaining stable on single node?

I am running a NPT molecular dynamics simulation. The
system contains a protein with 141 residues surrounded
by water making the total to 32714 atoms. I ran this
simulation at two places for 8ns. One as a serial job
and the other as a parallel job on 16 nodes. 
The protein remains stable all through for the serial
job but for parallel job the protein  opens up after
3ns of simulation and is never stable after that. 

All other conditions are exactly the same. Any help
would be highly appreciated. 


Akansha Saxena
Graduate Student
Department of Biomedical Engineering
Washington University in St Louis

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