Replica Exchange

From: Arturas Ziemys (ziemys_at_chbmeng.ohio-state.edu)
Date: Thu Oct 26 2006 - 10:53:16 CDT

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Hi,

We have cluster using PBS and we run NAMD with "run_namd *.namd > *.log".

>From the script "fold_alanin.conf" it is not clear which option I should use for 'spawn_namd_command':

1 - "# spread jobs across machines assigned by queueing system" with "$env(LSB_HOSTS) ]"

2 - "# spread jobs across machines assigned by queueing system" with "[read [open $env(HOST_FILE) "r"]] ]"

3- "# run parallel jobs - this may or may not work"

Each replica needs to be run in parallel, because the system is big. Which option should be chosen?

Best
Arturas

• Next message: Vishal Kopardé: "Ion-protein and protein-protein interactions"
• Previous message: Jacob Poehlsgaard: "Using/converting old extended top and par files?"
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• Reply: Vishal Kopardé: "Ion-protein and protein-protein interactions"
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