AW: NAMDEnergy: run with XSC file or not?

From: Norman Geist (
Date: Thu Nov 22 2012 - 00:40:21 CST



it's just what came to my mind when reading your post, I have never used
NAMDenergy. The only thing I can imagine is the periodic boundary condition.
I don't know where NAMDenergy gets the box dimensions from when they were
not set anywhere like by xsc. Possibly it's not using PBC then, which could
lead to non functional PME as it needs pbc which could clarify the energy


Good luck


Norman Geist.


Von: [] Im Auftrag
von Evgeny Bulat
Gesendet: Mittwoch, 21. November 2012 20:27
Betreff: namd-l: NAMDEnergy: run with XSC file or not?


Hey NAMD users,

I have a technical question regarding running NAMDEnergy to obtain
non-binding interactions between two molecules. I start VMD remotely via
command line and load up the appropriate psf and dcd files. After that, I
run a script that executes the following command for a bunch of pairs of
molecules in my system:

namdenergy -nonb -sel $sel1 $sel2 -ofile $output -tempname namd_nag1
-timemult 1 -stride 10000 -par [a bunch of param and toppar files] -pme
-extsys $xsc_file

NAMDEnergy outputs really nice and helpful energy graphs. However, when I
looked through some, I noticed that the initial binding energy is
occasionally really high, as in 60-70 kcals/mol! When I tried to figure out
why, one of the things I tried is running the above command without
specifying -extsys. That is:

namdenergy -nonb -sel $sel1 $sel2 -ofile $output -tempname namd_nag1
-timemult 1 -stride 10000 -par [a bunch of param and toppar files] -pme

Both are legit ways of running NAMDEnergy according to the manual. This
time, though, I got reasonable energies for the same pairs of molecules that
gave me really high, positive energies before. Just to clarify, the xsc file
I use is the one that preceeds the equilibration for which I'm running

Could anyone give me some guidance as to why specifying -extsys makes such a
big difference? Also, in light of this, which calculation should I trust

Thank you!


Jack Bulat
Dept. of Molecular and Cell Biology,
Chemical Biology Graduate Program,
UC Berkeley

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