Re: angle in colvars

From: Felipe Merino (felmerino_at_uchile.cl)
Date: Mon Nov 09 2009 - 06:19:03 CST

Indeed, using negatives force constants solved the problem.

thanks

Dimitar V Pachov escribió:
> Felipe,
>
> Try a negative force constant. We (mainly a colleague of mine) found the vectors defining the angle in the colvar module are 180 degrees inversed.
>
> Best,
> Dimitar
>
>
>
> ----- "Felipe Merino" <felmerino_at_uchile.cl> wrote:
>
> | From: "Felipe Merino" <felmerino_at_uchile.cl>
> | To: namd-l_at_ks.uiuc.edu
> | Sent: Sunday, November 8, 2009 10:52:10 PM GMT -05:00 US/Canada Eastern
> | Subject: namd-l: angle in colvars
> |
> | Dear all:
> |
> | I was planing to put a constraint on the angle between two domains of
> | a
> | protein using the colvars module. To test it i tried to constaint a
> | angle of a small system (deca-alanine). I also tried distance and
> | dihedral restraints which ran just fine. I used the following
> | colvarsconfig for the angle
> |
> | colvar {
> | name theta
> | outputAppliedForce yes
> | width 1
> | angle {
> | group1 {atomNumbers 99}
> | group2 {atomNumbers 44}
> | group3 {atomNumbers 4}
> | }
> | }
> |
> | harmonic {
> | colvars theta
> | centers 140
> | forceconstant 5
> | }
> |
> | , but while the value of the angle is initially very close to 140 it
> | goes reaches almost 180 in a few steps. If i move the center to 150 (i
> |
> | little higher that the initial value) it drops fast to near 0.
> |
> | i pasted the initial part of the trj file below
> |
> | # step theta fa_theta
> | 0 1.41022672562147e+02 -5.11336281073667e+00
> | 100 1.70516110530757e+02 -1.52580552653785e+02
> | 200 1.73020535100957e+02 -1.65102675504784e+02
> | 300 1.75996871130796e+02 -1.79984355653981e+02
> | .....
> |
> | So, i don't know what could be going wrong. Any suggestions would be
> | appreciated
> |
> | thanks in advance
> |
> | Felipe
> |
> | PS: By the way, i was using the last nightly build binary.
>
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:51:40 CST