Re: extracting interaction energies

From: Peter Freddolino (
Date: Mon Oct 01 2007 - 15:38:57 CDT

Hi Narender,
this is precisely what namdenergy
( is designed
for. Please note that namdenergy does not update the selection between
frames (an option to include this will be added to the next release of
vmd); this is only a problem if you use a selection that varies between
timesteps (eg, one with a cutoff). If you need such a selection, you can
currently use the text version of namdenergy within a loop (see the
documentation for more on running this mode):

package require namdenergy
set sel1 [atomselect top protein]
set sel2 [atomselect top "water and same residue as within 5 of protein"]

for {set i 0} {$i < [molinfo top get numframes]} {incr i} {
$sel1 frame $i
$sel2 frame $i
namdenergy -sel $sel1 $sel2 -nonb


Narender Singh Maan wrote:
> Hello,
> can someone please tell me how to extract vanderWaal's and
> Electrostatic interaction energies from MD simulation trajectories?
> (Not the one from the output file, that's for the system (?)
> (water-water, protein-water, protein-ions, water-ions, etc..), I am
> interested only in the vdw and electrostatic energies of the protein
> with its surrounding water/ions within a certain cutoff distance.
> Any suggestion/comment/help would be greatly appreciated.
> Thank you
> narender

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