Distance Constraints in ABF Simulation

From: Vince Cho (vince_at_fastmail.fm)
Date: Wed Dec 25 2013 - 05:31:26 CST

Hello All,

I am trying to calculate the PMF of my system via ABF method, using
dihedral angle as my reaction coordinate with colvars command. However,
I would also like to restrain some distances during this simulation.
>From the ABF documentation
(http://www.ks.uiuc.edu/Research/namd/2.6/ug/node35.html), I have found
that restraintList option was available, but when I tried it an error
occurred saying that this keyword cannot be recognised.

I have a feeling that when I load abf within colvars command, there is
only a limited number of commands that I can use within that, but I'm
not sure. Anyway, could you please take a look at my conf and in files
and see where it went wrong?

Here is how I call Colvars.in from my .conf file:

colvars on
colvarsConfig Colvars.in

And the Colvars.in file looks like:

colvarsTrajFrequency 500
colvarsRestartFrequency 5000

colvar {
  name phi

  width 0.5
  lowerboundary 3
  upperboundary 9
  lowerWallConstant 0.2
  upperWallConstant 0.2

  dihedral {
    group1 {
      atomsFile l1_atom.pdb
      atomsCol O
      atomsColValue 1.0
    }
    group2 {
      atomsFile l1_atom.pdb
      atomsCol O
      atomsColValue 2.0
    }
    group3 {
      atomsFile l1_atom.pdb
      atomsCol O
      atomsColValue 3.0
    }
    group4 {
      atomsFile l1_atom.pdb
      atomsCol O
      atomsColValue 4.0
    }
  }
}

abf {
   colvars phi
   fullSamples 500
   abf restraintList {
   dist1 {dist {P1 2 CA} {P5 2 CA} 40.0 16.0}
   dist2 {dist {P1 13 CA} {P5 13 CA} 40.0 16.0}
   dist3 {dist {P2 2 CA} {P6 2 CA} 40.0 16.0}
   dist4 {dist {P2 13 CA} {P6 13 CA} 40.0 16.0}
   dist5 {dist {P3 2 CA} {P7 2 CA} 40.0 16.0}
   dist6 {dist {P3 13 CA} {P7 13 CA} 40.0 16.0}
   dist7 {dist {P4 2 CA} {P8 2 CA} 40.0 16.0}
   dist8 {dist {P4 13 CA} {P8 13 CA} 40.0 16.0}
   }
}

And like I said above, the "restraintList" keyword doesn't seem to be
recognised.

Thanks in advance, and Merry Christmas to all!

-- 
  Wovon man nicht sprechen kann, daruber muss man schweigen.

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