NAMD pulling one domain

From: snoze pa (
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.


This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:22:26 CST