From: Chris Harrison (charris5_at_gmail.com)
Date: Thu Mar 07 2013 - 18:19:39 CST
You need to clarify which version of namd you're using and whether
you're using a shared memory machine or distributed cluster.
On Thu, Mar 7, 2013 at 4:16 PM, Martin, Erik W <Erik.Martin_at_stjude.org> wrote:
> Could someone who has experience running replica exchange simulations comment on the memory requirements of these type of simulations? Does it purely scale linearly with the number of replicas? For example, if it requires 450MB to run a traditional MD simulation on the structure, can I assume that it would take 4.5e4MB to run 100 replicas of this system? I can't seem to find any information searching on how namd handles this, but since it seems to just drive x number of different simultaneous simulations, this seems logical.
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-- Chris Harrison, Ph.D. NIH Center for Macromolecular Modeling and Bioinformatics Theoretical and Computational Biophysics Group Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 http://www.ks.uiuc.edu/Research/namd Voice: 773-570-6078 http://www.ks.uiuc.edu/~char Fax: 217-244-6078
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