Changing NAMD XY restraint

From: Beaven, Andrew (a607b333_at_ku.edu)
Date: Fri Aug 02 2013 - 16:29:05 CDT

Hi - is there a way I can continually update the target position for a harmonic restraint? I'm trying to restrain two protein monomers at the maximal distance away from each other. I see that I could simply use the numerical value of the initial 0.25*$boxa (which is ~18 ), but I'd like the target value to fluctuate with the box size during the simulation (since I'm starting from a non-equilibrated system). When I use the numerical value, the job runs and appears to keep the monomers in the desired locations, but as mentioned, this isn't exactly what I want

In my NAMD input file (along with the other simulation variables), I use:

colvars on
colvarsConfig /path/restraint.col

The /path/restraint.col file is shown below.

Thank you,

Andrew

################################################

Colvarstrajfrequency 100
Colvarsrestartfrequency 100

colvar {
   name proa_rest
   distanceXY {
      ref {
         dummyAtom ( -0.25*$boxa, -0.25*$boxa, 0.000 )
      }
      main {
         atomsFile /path/proa.ref
         atomsCol B
         atomsColValue 1.0
      }
   }
}

colvar {
   name prob_rest
   distanceXY {
      ref {
         dummyAtom ( 0.25*$boxa, 0.25*$boxa, 0.000 )
      }
      main {
         atomsFile /path/prob.ref
         atomsCol B
         atomsColValue 1.0
      }
   }
}

harmonic {
   colvars proa_rest
   centers 0.0
   forceConstant $fc
}

harmonic {
   colvars prob_rest
   centers 0.0
   forceConstant $fc
}

################################################

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