Re: periodic boundary conditions in namd energy calculation

From: Michael S. Sellers (Cont, ARL/WMRD) (
Date: Tue Nov 30 2010 - 14:06:09 CST



XSC file (-extsys FILE): Use the specified xsc file to set up a periodic


If your .xsc file was generated with PBCs enabled, then PBCs will be
used in the VMD calculation.


Lan Hua wrote:
> Dear NAMD users,
> I am wondering if the periodic boundary conditions have been
> applied in the following calculation of interaction energy using
> namdenergy plugin in VMD. It was done in text interface. The two
> atom selections are:
> set sel1 [atomselect top "resid 100 and water"]
> set sel2 [atomselect top "not (resid 100 and water)"]
> The main options I specified are:
> -elec -vdw -sel $sel1 $sel2 -cutoff 12 -switch 10 -extsys *.xsc
> I want to know whether the obtained vmd energy and the electrostatic
> energy (with pme (-pme), or without) were calculated under the
> periodic boundary conditions. Are the interactions between (resid 100
> and water) and its images included in the calculation?
> Thank you very much!!!
> Lan

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