Help With colvars/abf Please

From: Angelo Rossi (
Date: Sun Jan 30 2011 - 07:09:41 CST


I am working with a lipid bilayer system with a water layer on each side of
the bilayer. To this lipid bilayer system,a transmembrane protein (channel
protein) has been added. The entire system spans from -50 A to +50 A along
the z-axis. The system has been equilibrated with namd in hexagonal
symmetry using either *useConstantRatio* or* useConstantArea* (Both of these
work well.) The temperature is rock solid at 300K.

The idea is now to pass permeant molecules through the channel and compute
the pmf as well as other properties.

When the first permeant molecule is placed in the system above and
equilibrated, it remains at around an average value of -20 A along the

Now here is the colvars input:

*Colvarstrajfrequency 100
Colvarsrestartfrequency 1000
colvar {
  name ProjectionZ
  width 2.0
  lowerboundary -10.0
  upperboundary 0.0
  lowerwallconstant 10.0
  upperwallconstant 10.0
  distanceZ {

  ref {
       atomsFile file.ref
       atomsCol B
       atomsColValue 1.0

  main {
# O4 O11 O12 O13 O14 O15
   atomNumbers 243930 243951 243972 243993 244014 244035
abf {
  colvars ProjectionZ
  fullSamples 500

The above colvars input is based on the aspect of the abf tutorial which
deals with methane hydration which is quite clever. Thus, my reference
coordinates are related to the top water layer around 50 A. The idea is to
have the permeant molecule travel through the channel and end up in the top
water layer while starting near the bottom layer. The oxygen atoms given
above are at the center of the permeant.

But look at the output:

        # step ProjectionZ
           0 4.64057200542220e+01
         100 4.62444387277113e+01
         200 4.60430582871365e+01
         300 4.57030585750052e+01
         400 4.53190819052589e+01
         500 4.50002912600680e+01
         600 4.47016047389293e+01
         700 4.44303855400716e+01
         800 4.41026610823705e+01
         900 4.38053772690827e+01
---------- snip snip snip ----------------------
       49300 2.96348802222812e+00
       49400 2.85421393614985e+00
       49500 2.55888925656819e+00
       49600 2.47146058653122e+00
       49700 2.42611123875734e+00
       49800 2.48713556793857e+00
       49900 2.53229282527830e+00
       50000 2.43943427282846e+00

Why is it doing this?

Why is the colvars calculation starting at the TOP of the channel when I
gave it instructions to perform the calculations between -10 and 0?

Of course all the other files look like the pmf file below:
# xi A(xi)
       -10 0
        -8 0
        -6 0
        -4 0
        -2 0
         0 0

There are no "hits" because the trajectory is traversing the upper channel
and not where it should be.

I understand that I am doing something incorrect here and would appreciate
any help you can provide.

Kind regards,


p.s. This is one of many trial runs that I performed.

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