SMD with colvar not working

From: Dhiraj Srivastava (
Date: Tue Apr 24 2018 - 00:21:43 CDT

   I am trying to pull an alpha helix of my protein using colvar component
distanceZ. however it seems that its not able to pull it out of my protein.
the helix is slightly curved and it seems to be able to straighten it up
during the first picosecond of simulation but after that there it seems to
stay at its place. below is my script. I have doubt about reference
position. I am choosing entire helix to apply pulling force. and I am
choosing entire helix as reference position. is that correct way of doing
SMD with distanceZ colvar. my final goal is to apply rotation and pulling
force at the same time. rotation is working.


colvar {
       name dist
       outputAppliedForce on
       width 0.1
       lowerBoundary 0.0
       upperBoundary 30
       hardLowerBoundary yes
       hardUpperBoundary yes

       distanceZ {
                  main {
                        psfSegID AP1
atomNameResidueRange CA 211-235
 ref {
                       psfSegID AP1
      atomNameResidueRange CA 211-235
  axis { (-0.22284841537475586, 0.4576619863510132, 0.8607462048530579)}
forceNoPBC no
oneSiteSystemForce no

harmonic {
name steery
        colvars dist
forceConstant 1
centers 0
targetCenters -30
targetNumSteps 100000
outputCenters yes
outputAccumulatedWork yes

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