Relaxed dihedral scans (or how to constrain a dihedral angle to a changing value).

From: Ajasja Ljubetič (
Date: Thu Oct 21 2010 - 08:45:43 CDT

Dear all,

I am currently running a rigid multidimensional dihedral scan of a spin
label. I generate the conformations using VEGA ZZ and than extract the
energies with namd using:

while { ![coorfile read] } {
  # Set firstTimestep so our energy output has the correct TS.
  firstTimestep $ts
  # Compute energies and forces, but don't try to move the atoms.
  run 0

  incr ts 1

Would it be possible to run a relaxed dihedral scan in a similar manner.
I tried putting "minimize 100" after each "run 0", which works in a manner.
After adjusting *DCDfreq* to 101 I get only minimal structures in the DCD.
(By the way - it seems that *outputEnergies *has no efect on the number of
energies printed during minimization)

I would like to be able to restrain the dihedral being scanned. I think that
neither tclForces or the ABF module work during minimization. Can extraBonds
or *consref *be changed between runs? Are there any other options?

(As a last resort I can always write N seperate pdb files.)

Best regards,

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