From: Atreya Dey (
Date: Fri Nov 20 2015 - 01:49:58 CST


I have a dcd file obtained by an MD simulation of two proteins binding to
each other. I wish to calculate the energy between a set of pairs amino
acids in each of the proteins (Each pair having one amino acid from one
protein). Now my selection of the amino acids is very strict, I want to use
only those pairs of amino acids which are within 8A of each other. I want
do this calculation only after 200 frames in the dcd file. But, by that
time the set of pairs will have changed as the amino acids will move, so. i
need to supply a new set of pairs of amino acids to namenergy.

I would like to know when I am trying to use namdenergy after a gap of 200
frames and I am supplying new selections every time, what should I do? I
know the -updatesel parameter exists, but I would like to know how to use
it properly.

Thanking you in advance,

Atreya Dey,
UG Programme,
IISc - Bangalore