using colvars to constrain two atoms in a direction

From: Hamed Fadaei (
Date: Wed Dec 14 2016 - 10:15:20 CST

Dear NAMD usrs,

I am trying to simulate a a drug translocationg from a membrane. The drug
is much longer in one direction and its orintation can be defined by a
single vector connecting two atoms (atom numbers 20 and 28 in my system).

Now I need to constrain this vector with respect to the Z axis at different
angles by applying forces to these two atoms. I don't want to add any extra
constraints to the position of the atoms and drug can be free to move as
long as it keeps its angle with Z axis fixed.

I tried to use "tilt" colvar by giving two ref points to define Z axis and
then constraining that tilt colvar to a harmonic :

colvar {

  name tilt1

       tilt {

       atoms {

            atomNumbers {

                 28 20



       refPositions (0,0,0) (0,0,1)



harmonic {

  colvars tilt1

  centers -0.9

  forceConstant 0.0


But when I run it, the system kinetic energy and temperature come out as
"nan" at step zero and I get the following error at the step one:

colvars: Too many iterations in routine jacobi.

FATAL ERROR: Error in the collective variables module: exiting.

Unfortunately I couldn't find anything related to that so I would be so
glad if you can help me. Besides, is this the best way to use tilt colvar
for my purpose or there might be a better way?



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