From: snoze pa (snoze.pa_at_gmail.com)
Date: Mon Aug 27 2012 - 14:36:34 CDT
Dear NAMD users,
I am working on a multi domain protein. Protein domains are similar to
immunoglobin but instead of pulling one residue( i.e applying pulling force
at one residue) i want to pull one complete domain. Is it possible using
SMD in NAMD? So far I am trying following protocol:
1. Calculate center of mass (CM) of a domain of interest and then pull the
CM in desired direction.
Is this approach is correct?
Thank you very much for your attention.
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