Re: angle in colvars

From: Dimitar V Pachov (dpachov_at_brandeis.edu)
Date: Sun Nov 08 2009 - 22:17:20 CST

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.

-- 
========================================================
Dimitar V Pachov
PhD Candidate
Physics & Biochemistry Department     Phone: (781) 736-2326
Brandeis University, MS 057           Email: dpachov_at_brandeis.edu
========================================================

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