mapping of force vectors during SMD

From: Jeff Forbes (
Date: Wed Apr 22 2009 - 13:42:23 CDT


I am interested in how forces are propagated though a protein
during a SMD simulation. From what I understand, tclforces can be used
to write out force vectors for individual atoms during a simulation.
If one were to obtain these force vectors for the backbone atoms, I
assume that the
sum of these vectors should be close to the force calculated from the
virtual spring
pulling on the protein. What I would like to do is to show the force
vectors on the structure
of the protein at different points, similar to a weather map with the
arrows showing the
strength and direction of the winds. Has anyone done something like
this for a SMD
simulation of a protein unfolding? Suggestions are welcome.

Jeffrey G. Forbes, Ph.D.
Staff Scientist
Muscle Proteomics and Nanotechnology Section
Laboratory of Muscle Biology
National Institute of Arthritis and
     Musculoskeletal and Skin Diseases
National Institutes of Health
Department of Health and Human Services
50 South Drive
Building 50, Room 1316
Bethesda, MD 20892-8024
Voice: 301-451-9535
FAX: 301-402-0009

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