From: Subbarao Kanchi (ksubbu85_at_gmail.com)
Date: Thu Oct 13 2016 - 19:20:39 CDT
Hi Brain Radak,
you could extract the pair interactions between the
two groups in NAMD by using as follow.
pairInteraction on
pairInteractionFile pair.pdb # this is the file where you provide the group
numbers
pairInteractionCol B # we use the B-Factor column to specify which atoms
belong to group 1 & 2
pairInteractionGroup1 1 # flag to include atoms in group 1
pairInteractionGroup2 2 # flag to include atoms in group 2
Cheers
Subbarao Kachi
On Thu, Oct 13, 2016 at 9:49 PM, Brian Radak <bradak_at_anl.gov> wrote:
> Is there an elegant way to get average energies via Tcl? The average
> instantaneous temperature and pressure are obviously available via the
> normal callback, but it doesn't look like total energy is, for example.
>
> Repeatedly calling "run [outputEnergies]" and then accumulating a sum as a
> Tcl variable works just fine and doesn't seem to be particularly low
> performance (for reasonably values of outputEnergies), but it does seem a
> bit inelegant.
>
> Regards,
> Brian
>
> --
> Brian Radak
> Postdoctoral Appointee
> Leadership Computing Facility
> Argonne National Laboratory
>
> 9700 South Cass Avenue, Bldg. 240
> Argonne, IL 60439-4854
> (630) 252-8643
> brian.radak_at_anl.gov
>
>
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