Scripting: Handle for energy terms in the PSF file?

From: Chang, Christopher (
Date: Mon Dec 10 2007 - 21:18:24 CST



   I am testing dihedral parameters, and am encountering nan's in the
first energy minimization step associated with the dihedral energy term.
I would like to dump out the associated dihedral energy for every term
in the associated PSF file to track down the problem(s), but I don't
know what the handles are for this. So, along the pseudocode lines of


set temp [atomselect top "protein"]

for PSF_dihedral_term in $temp:

   measure energy $PSF_dihedral_term;


I've seen the NAMD PairInteraction option, but I'd still need a handle
for the terms in the PSF file. mdenergy from Jan Saam is another option,
but I would have to merge two parameter files, which I'd rather avoid.


How do the pros do this?


NAMD 2.6, 64-bit








Christopher H. Chang, Ph.D.
Scientist II
National Renewable Energy Laboratory
1617 Cole Blvd., Mail Stop 1608
Golden, CO 80401
Phone (303) 275-3751
Fax (303) 275-4007


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