need help in using colvars option

From: sudipta (
Date: Mon Aug 27 2012 - 17:41:51 CDT

Hi All,

I need to perform a restrained simulation of protein molecule. In this
regard, I need your help. To perform that simulation, I have chosen two
groups of protein atoms and COM distance between these two groups of atoms
is the collective variable. The input parameters are given below,

colvarsTrajFrequency 100
colvarsRestartFrequency 100

colvar {
   name comdis

   width 5.0

   lowerboundary 0
   upperboundary 133.0

   lowerWallConstant 0.1
   upperWallConstant 0.2

   outputAppliedForce on
   outputVelocity on
   outputSystemForce on

   distance {

      group1 {
         atomnumbers {3442 4835}
      group2 {
         atomnumbers {4137 4140}

I have manually calculated the COM distance between these two group of
atoms and the value is significantly differ with the namd output which is
written in .colvars.traj file. The two values are 132.33 (35.3 with PBC) A
and ~60 A. My aim is to sample the protein molecule in such a manner where
the distance between those two defined group of atoms of the protein
molecule fluctuate around 132.33 A with some standard deviation (say 5 A).
So how to reach my aim. Any suggestion will be highly appreciated.

Thanks in advance

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