Spinangle with refgroup : Warning: discontinuous rotation!

From: nicolas martin (nicolasmartin973_at_gmail.com)
Date: Mon Apr 07 2014 - 11:33:50 CDT

Dear NAMD users,

As part of my project, I planned to compute the spinangle of the upper part
of the protein and set the lower part as a reference. To develop my method
i chose to work with deca-alanine working with one extremity, computing the
spinangle of the last part of ALA10 around an axis, defined as the axis
going through one bound nearby. This spinangle is then restrained to obtain
a rotation of the mobile part of my selection. Exactly as one would do
computing a dihedral angle and restraining it to explore [-180;180[.

I tried to be as clear as possible to explain what I aim to do, but I am
sure that is no trivial thing to get. Anyway my point by seeking for help
is that I cannot success in running long simulations of this system. For
the short ones, I got some "Warning: discontinuous rotation!" but the
simulation can end properly. When I try to elongate the simulation, the
velocities of random atoms happens to be too high so does the temperature
of the system and the calculation crash before term.

I figured out by deduction that this "discontinuous rotation" was due to a
bestfit step (which could occur in both spinangle and refgroup) but since I
do not really understand why I might be mistaken. Maybe this is the way I
want to restrain and compute this spinangle which is totally wrong. You
will find below the definition of my colvar.

Hoping you can help me on this one, bests,

Nicolas Martin
Laboratoire d'Ingenierie des Fonctions Moleculaires
Universite de Strasbourg

colvar {
  name spinangle
  spinangle {
    atoms {
      atomNumbers 92 93 94 95 96 99 100 101 102 103 104 # measure group
      centerReference on
      rotateReference on
      refPositionsGroup { # reference group
        atomNumbersRange 1-91
     refPositionsFile input/ref.pdb
     refPositionsCol O
     refPositionsColValue 1.00
  refPositionsFile input/mesure.pdb
  refPositionsCol O
  refPositionsColValue 1.00
  axis (-0.476,0.644,1.189) # rotation axis defined along a bond
harmonic {
       name harmonic
       colvars spinangle
       forceConstant 0.0060923 # this should be equal to 10kcal/mol/radian
       centers -180
       targetCenters 180
       targetNumSteps 50000
       targetNumStages 37

colvar {
  name rmsd
  rmsd {
    atoms { atomNumbersRange 1-91 # reference part is restrained by RMSD
  refPositionsFile input/ref.pdb
harmonic {
  colvars rmsd
  forceConstant 3000
  centers 0

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