Re: periodic boundary conditions in namd energy calculation

From: Michael S. Sellers (Cont, ARL/WMRD) (michael.s.sellers.ctr_at_us.army.mil)
Date: Tue Nov 30 2010 - 14:06:09 CST

Lan,

This:

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

From:

http://www.ks.uiuc.edu/Research/vmd/plugins/namdenergy/

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

-Mike

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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