From: Felipe Merino (felmerino_at_uchile.cl)
Date: Sun Nov 08 2009 - 21:52:10 CST
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.
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