Re: angle in colvars

From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Mon Nov 09 2009 - 09:09:17 CST

Hi,
Thanks to Dimitar for this report. We'll look into the code, so that
when the next version comes out, you may have to go back to positive
force constants...
Jerome

2009/11/9 Felipe Merino <felmerino_at_uchile.cl>:
> 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.
>>
>>
>
>

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