From: Dolan, Michael (NIH/NIAID) [C] (dolanmi_at_niaid.nih.gov)
Date: Wed Nov 26 2008 - 13:36:51 CST
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.
Michael A. Dolan, Ph.D.
Contractor, Lockheed Martin
Computational Structural Biologist
Bioinformatics and Computational Biosciences Branch (BCBB)
31 Center Dr., Room 3B62
Bethesda, MD 20892-0485
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