colvars to restrain peptide close to lipid

From: Chitrak Gupta (
Date: Wed Apr 26 2017 - 15:01:23 CDT

Hi NAMD users,

I am simulating a peptide-lipid system where the peptide is placed on the
top of the lipid. To keep the peptide from interacting with the bilayer of
the periodic image, I used the upperWallConstant colvars feature, defined
on the "distanceZ" between a peptide atom and a lipid atom. Here is the
script I used

colvar {
          distance Z {
                            ref {
                                  # This file has the "beta" column of the
lipid atom set to 1, everything else set to 0
                                   atomsFile lipidBeta.pdb
                                   atomsCol B
                                   atomsColValue 1.0
                          main {
                                   # This file has the "beta" column of the
peptide atom set to 1, everything else set to 0
                                   atomsFile peptideBeta.pdb
                                   atomsCol B
                                   atomsColValue 1.0

       upperBoundary 70.0
       upperWallConstant 1000.0

However, in the simulation, I do find the colvars distance transiently
crossing the upper boundary (which is ok for my simulation), and then
eventually the peptide starts interacting with the lipid in the periodic

Does anyone know if I implemented the colvars correctly?

Also, I had "wrapAll on" which meant once the peptide started interacting
with the periodic image, it came to the bottom of the peptide and now the
colvars distance had a negative value, which obviously was still "within"
the upper bound. Should I also use a lowerWallConstant to take care of this?

Thanks for the help,

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