PMF calculations between membrane and nano particle simulations

From: Subbarao Kanchi (
Date: Thu Jul 03 2014 - 15:58:23 CDT

Dear All,
              I am trying to do umbrella sampling simulations by using
colvars in NAMD. I have taken the reaction as the distance between
 membrane center and nano particle center along membrane normal (Z-axis).
I have used the colvar input file as shown below.

colvarsTrajFrequency 100
colvarsRestartFrequency 100

colvar {

        width 1.0
        name lipid
        distancez {
                   main { atomNumbersRange 60417-61701} # atoms of
                   ref {
                          atomsFile com_lipid.pdb

                          atomsCol B
                          atomsColValue 1.0
                   axis (0.0, 0.0, 1.0)

harmonic {
          colvars lipid
          centers 29.0
          forceConstant 4.0
          targetCenters 30.0
          targetNumSteps 200000

This colvar is working fine in keeping the distance between center along
 z-axis. I kept the nano particle at the center of membrane but in dynamics
it is moving in xy plane of the particular bin (z=30.0) and coming to edges
of simulation box. I have few doubts regarding this.

1) The nano particle coming at the edges of box. Is this cause the
artifacts in the PMF calculations ?

2) If yes, how to add more restrains to keep nano particle just above the
membrane center and how to incorporate in WHAM calculations ?

I will appreciate any suggestions in this regard.


This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:22:34 CST