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

From: Jim Phillips (
Date: Fri Oct 22 2010 - 10:30:59 CDT

TclForces should work during minimization as long as you also calculate
the correct energy to go along with the force (i.e., the added force is
the negative gradient of the added energy). The minimizer relies on
energies during its line searches.


On Thu, 21 Oct 2010, Ajasja Ljubeti~M wrote:

> 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,
> Ajasja

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