From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Tue Feb 12 2013 - 07:08:35 CST
Hi George,
SMD would be one option for applying a torque, however, this assumes a rigid-body rotation, so it is a also a conformational restraint.
You may want to apply a torque that has no bearing on internal degrees of freedom (ie protein conformation); that is possible thanks to the Collective Variable module. Specifically, you want a moving harmonic restraint applied to a spinAngle variable. That variable will track rotations based on a fit to the initial coordinates (see user's guide for details).
The colvars input might look like this (with extra comments):
-----
colvarsTrajFrequency 100 # output values every 100 steps
colvar {
name spin
outputAppliedForce on # keep track of bias force on this variable
spinAngle {
atoms {
atomsfile system.pdb # Select biased atoms from this file
atomsCol B # based on column B
atomsColValue 1 # atoms flagged with 1
}
refPositionsFile system.pdb # Fetch initial positions from this file
refPositionsCol B # Same flags as above
refPositionsColValue 1
}
# Here we assume the rotation axis is z (default value)
# otherwise specify "axis"
}
harmonic { # Define a moving harmonic restraint
colvars spin # acting on colvar "spin"
centers 0 # go from 0 degree rotation...
targetCenters 180 # ... to 180 degrees
targetNumSteps 10000000 # in 10 million steps
forceConstant 0.5 # unit is kcal/mol/degree^2
}
-----
I hope this is enough to get you started.
Cheers,
Jerome
----- Mail original -----
>
> Hello
>
> Sorry for posting about this again, but I got no reply.
>
> I just wanted to know how can we apply a torque to a part of a system
> a
> using NAMD.
>
> Is this done through the rotating constraints? (flags rotConstraints,
> rotConsAxis, rotConsPivot and rotConsVel options in the conf file)
>
> Do we also need the SMD options in the conf file?
>
> I am a bit confused because in this link
>
> http://www.ks.uiuc.edu/Research/f1atpase/
>
> it is mentioned "We use steered molecular dynamics (SMD) simulations
> to
> apply a torque to F1..."
>
> Thanks.
>
> Dr. George Patargias
> Postdoctoral Researcher
> Biomedical Research Foundation
> Academy of Athens
> 4, Soranou Ephessiou
> 115 27
> Athens
> Greece
>
> Office: +302106597568
>
>
This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:22:57 CST