RE: center of mass for SMD

From: JC Gumbart (
Date: Wed Feb 11 2009 - 22:44:01 CST

You can do this using VMD. After making the appropriate atom selection, use
the command "measure center $sel weight mass". Your idea seems reasonable
to me.


From: [] On Behalf
Of Falgun Shah
Sent: Tuesday, February 10, 2009 5:52 PM
Subject: namd-l: center of mass for SMD


Dear NAMD user

I am planning to run SMD simulation of protein-peptide complex in NAMD. I am
having difficulties in deciding egress direction in NAMD

I want to select c-alpha atoms of two residues of my peptide as SMD atoms. i
want to know how to calculate the center of mass for this two residues only.
Similarly, i want to keep 3 residues of protein as fixed atoms and
calculating center of mass for that. i think by this way i will get two
different coordinates and from that i will be able to calculate pulling
direction as described in NAMD tutorial. Please let me know how to do it. is
it the correct way? if not, please give me few more suggestions how to
calculate the direction. Thanks in advance

Falgun H shah
PhD candidate (3rd year)
Department of Medicinal Chemistry
2028, Natural Product Center
University of Mississippi
Ph No: 6629151286(O)
          662 801 5667(M)

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