From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Thu Oct 25 2018 - 18:29:47 CDT
Hi Nick,
Just to expand on Giacomo's answer, this is just one of those things with a CHARMM force field. Equilibrated systems are stable because the electrostatics are negative and about an order of magnitude larger in size than the VDW term. So VDW>0 is perfectly normal.
-Josh
On 2018-10-25 15:39:12-06:00 owner-namd-l_at_ks.uiuc.edu wrote:
Hi Nick, the reply to one of the messages:
On Thu, Oct 25, 2018 at 4:00 PM Nick Palmer <tuf90798_at_temple.edu<mailto:tuf90798_at_temple.edu>> wrote:
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: Mon Dec 31 2018 - 23:21:27 CST
https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2013-2014/2290.html
sounds like a very plausible explanation.
Hello everyone,
When running simulations, is it typical to have slightly higher than positive VDW energies?
After running NAMDEnergy on my system I found that the energies pretty consistently are in the range of +5 to +40. I read some previous posts which I'll link to below, but I don't think there was a resolution to them.
https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2013-2014/2289.html
https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2005-2006/3358.html
Thank you in advance
--
Nicholas J. Palmer
--
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU