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From: Basak Isin (isinbasak_at_yahoo.com)
Date: Fri Aug 02 2013 - 16:35:11 CDT

 

----- Original Message -----
From: "Beaven, Andrew" <a607b333_at_ku.edu>
To: "<namd-l_at_ks.uiuc.edu>" <namd-l_at_ks.uiuc.edu>
Cc:
Sent: Friday, August 2, 2013 2:29 PM
Subject: namd-l: Changing NAMD XY restraint

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 Å), 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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