RE: Positive VDW energies

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:
https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2013-2014/2290.html%7Cc0ad824fd5ea4540637008d63ac24b86%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636761003513962683&sdata=5JJsRCpHWGlfFYRPhvBZ9XnLjTnsBXDAhrgq6Xg07XA%3D&reserved=0>
sounds like a very plausible explanation.

On Thu, Oct 25, 2018 at 4:00 PM Nick Palmer <tuf90798_at_temple.edu<mailto:tuf90798_at_temple.edu>> wrote:
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%7Cc0ad824fd5ea4540637008d63ac24b86%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636761003513962683&sdata=HLDMDRNBJUt9n36h4iTef0H6pXMEZn6t1DR8PDsDaDE%3D&reserved=0>
https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2005-2006/3358.html%7Cc0ad824fd5ea4540637008d63ac24b86%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636761003514118942&sdata=BKxOF5N5e%2BJF5mpoHnMk0aSqq7PCYQuLDHd1ui7hFvQ%3D&reserved=0>
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/Q3TBQUt2Q50NseQjyK4p1IcB%2B4bwl4JI0g%3D&reserved=0>
https://github.com/giacomofiorin2&sdata=BPAcpT9EDr3foHodrM%2BLdLC5B5VVHzQYzmE9LdXCdMM%3D&reserved=0>

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