force potentials for residue-based CG

From: Dolan, Michael (NIH/NIAID) [C] (dolanmi_at_niaid.nih.gov)
Date: Wed Nov 26 2008 - 13:36:51 CST

Hello,

Am I on the right track?

I have run a residue-based coarse-grained MD simulation of a small protein in a box of explicit water, but see the amino acids "collapse" into one another, not maintaining what I think is an appropriate distance between the backbone (BB) bead and the sidechain bead. I am using a set of topologies made by TCBG at UIUC and a parameter file (di25.par) derived from Marrink et al, 2004), but I believe that I need to modify some force potentials in the NAMD source code and recompile in order to keep the BB and sidechain beads more of a distance apart.

I should probably start with ComputeBonds.C ... Correct?

Any guidance is most welcomed.

Mike

-----------
Michael A. Dolan, Ph.D.
Contractor, Lockheed Martin

Computational Structural Biologist
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH

31 Center Dr., Room 3B62
Bethesda, MD 20892-0485
Fax:
http://bioinformatics.niaid.nih.gov

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