From: Chang, Christopher (Christopher_Chang_at_nrel.gov)
Date: Mon Dec 10 2007 - 21:18:24 CST
Hi,
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
Opteron
Linux
Thanks,
Chris
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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