Re: Spinangle with refgroup : Warning: discontinuous rotation!

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Apr 09 2014 - 11:18:13 CDT

Hello Nicolas, here are some suggestions:
- please send all your emails to the mailing list, not only part of them;
- butane is a tiny molecule, but still fairly flexible: please try a really
rigid one such as benzene or phenol instead of setting constraints;
- when you constrain/restrain the positions of heavy atoms, the two
terminal methyl groups can still rotate;
- a dihedral angle and a spinangle are two different quantities: your setup
is only for the latter, if you wish to define the dihedral C1-C2-C3-C4, you
should do so by using a "dihedral" function.

Regards,
Giacomo

On Wed, Apr 9, 2014 at 11:40 AM, nicolas martin
<nicolasmartin973_at_gmail.com>wrote:

> Dear Giacomo,
>
> After reading your message I went back to my first idea which was
> developing my method on a way smaller molecule : butane. As you mentioned I
> tried to solve the problem of RMSD on both group by restraining them. I
> still have those Warnings and actually cannot align my reference group in
> VMD. In another hand, I can see clearly the spinangle colvar going from 0
> to 40 as asked but the dihedral angle itself is not moving... I think this
> might be due to a failure of the alignment.
>
> Here is the input file :
>
> colvar {
> name spinangle
> spinangle {
> axis (-1.408,-0.537,-0.317) # axis C2 C3
>
> atoms {
> atomNumbers 11 12 13 14 #..moving group
> centerReference on
> rotateReference on
> refPositionsGroup { #..reference group
> atomNumbers 1 5 8
>
> }
> refPositionsFile input/ref.pdb
> refPositionsCol O
> refPositionsColValue 1.00
> }
>
> refPositionsFile input/ref.pdb
>
> }
> }
> harmonic {
> name harmonic
> colvars spinangle
> forceConstant 0.0060923
> centers 0
> targetCenters 40
> targetNumSteps 1000
> targetNumStages 11
> }
> colvar {
> name rmsd
> rmsd {
> atoms { atomNumbers 11 12 13 14 }
> refPositionsFile input/ref.pdb
> }
> }
> harmonic {
> name rmsd_hamonic
> colvars rmsd
> forceConstant 100
> centers 0
> }
>

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