set dummyAtom position changing

From: christos.lamprakis_at_dcb.unibe.ch
Date: Fri Apr 01 2011 - 09:44:39 CDT

Dear NAMD users/developers,

I would like to use the component dihedral (colvar) in order to
monitor the rotation of a molecule. I was thinking to define three
points on the molecule (group1-group3) and a dummy atom (group4) out
of the molecule in such a way that g4_pos.x = g3_pos.x, g4_pos.y =
g3_pos.y and g4_pos.z = g3_pos.z -1. In other words, group.3 and
group4 will have the same x and y and different z.
I think I have to change the line 190 of colvarcomp_angles.C in
order not to return the reference position of the dummy atom but
update it following group3 :

  //cvm::atom_pos const g4_pos = group4.center_of_mass();
   cvm::atom_pos const g4_pos = (g3_pos.x, g3_pos.y, g3_pos.z -1)

Is this syntax going to work? Is there any other point that it should
change? I would welcome any suggestion before start bothering people
with compiling.

Many thanks in advance,
Christos

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:23:47 CST