Constraining center of mass of monomers

From: S.K. Ghosh (skg30_at_cam.ac.uk)
Date: Wed Jul 16 2008 - 17:45:57 CDT

Hi users,

I want to constrain the centers of mass of each of the three monomers of a
tetramer protein to its initial position with a spring constant k and pull
a single atom of the 4th monomer at a constant velocity. I am trying it to
do it on the lines of the attached script (found with Stretching
Deca-Alanine tutorial).

1. Instead of just a single atom (id1) as below (excerpt from attached
script), can I add all atoms of a particular segname to the group grp1?
Could you please suggest how.

set id1 [atomid BH 1 N]
set grp1 {}
lappend grp1 $id1
set a1 [addgroup $grp1]

2. Then, once I add all atoms to group grp1, I guess "addgroup" finds the
center of mass of the group. Could you please confirm whether this
understanding is correct.

3. Does the following command (again from attached script) apply the same
force on all atoms in group grp1?

addforce $a1 $f1

Thanks very much.

Sourav

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