From: David A. Horita (dhorita_at_wfubmc.edu)
Date: Wed Nov 25 2009 - 13:55:56 CST
Hi,
I'm trying to prevent a protein from rotating during an MD simulation - the 2.7b2 "hints" that this can be done with the colvars orientation function. I was wondering if some one could provide more hints (or a script). So far I have:
colvar {
name NoRotation
width 1.0
orientation {
atoms {
atomsFile constrained.pdb
psfSegID P1 P2 P3 O1
}
refPositionsFile constrained.pdb
refPositionsCol B
}
}
harmonic {
name pot
colvars NoRotation
forceConstant 1.0
centers (1, 0, 0, 0)
}
which doesn't give error messages but also doesn't proceed past the first energy step (after this I get one ETITLE and one ENERGY line). Any suggestions as to what I'm leaving out/doing wrong would be appreciated.
Thanks,
Dave
(colvars section of log file follows)
colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 20090807.
colvars: # analysis = off [default]
colvars: # colvarsTrajFrequency = 100
colvars: # colvarsRestartFrequency = 100
colvars: The restart output state file will be "md1.restart.colvars.state".
colvars: The trajectory file will be "md1.colvars.traj".
colvars: The final output state file will be "md1.colvars.state".
colvars: ----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = NoRotation
colvars: Initializing a new "orientation" component.
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: Initializing atom group "atoms".
colvars: Atom group "atoms" defined, 109450 initialized: total mass = 673500.
colvars: # refPositions = [default]
colvars: # refPositionsFile = constrained.pdb
colvars: # refPositionsCol = B
colvars: # refPositionsColValue = 0 [default]
colvars: Centering the reference coordinates: it is assumed that each atom is the closest per
iodic image to the center of geometry.
colvars: # closestToQuaternion = ( 1 , 0 , 0 , 0 ) [default]
colvars: All components initialized.
colvars: # width = 1
colvars: # expandBoundaries = off [default]
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = off [default]
colvars: # outputSystemForce = off [default]
colvars: # outputAppliedForce = off [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables initialized, 1 in total.
colvars: ----------------------------------------------------------------------
colvars: Initializing a new "harmonic" instance.
colvars: # name = pot
colvars: # colvars = { NoRotation }
colvars: # forceConstant = 1
colvars: # centers = { ( 1 , 0 , 0 , 0 ) }
colvars: # targets = { ( 1 , 0 , 0 , 0 ) } [default]
colvars: # forceConstantTarget = 0 [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables biases initialized, 1 in total.
colvars: ----------------------------------------------------------------------
colvars: Collective variables module initialized.
colvars: ----------------------------------------------------------------------
Info: Startup phase 7 took 82.655 s, 153.653 MB of memory in use
Info: Startup phase 8 took 0.000155926 s, 153.78 MB of memory in use
Info: Finished startup at 86.3973 s, 153.78 MB of memory in use
TCL: Running for 5000000 steps
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