umbrella sampling

From: ipsita basu (
Date: Wed Aug 22 2012 - 01:52:14 CDT

I want to observe a protein penetration into membrane,that's why I
want to do umbrella sampling simulation. The configuaration file where
the umbrella sampling is enabled is given below:
colvarsTrajFrequency 200
colvar {
  width 1.0
  name distanceZ
  distance {
    group1 {
      atomNumbers 97280
    group2 {
      atomNumbers 1235
harmonic {
  name lenpot
  colvars distanceZ
  centers 10.0
  forceConstant 1.0
  targetCenters -10.0
  targetNumSteps 2000000
  targetNumStages 30
where I put the value of z coordinate of 97280th atom in centers
(centers 10.0). And I want to fix the process for the 97280th atom to
reach from 10.0 to -10.0(targetCenters) in 2000000 steps.
Am I doing right thing or not? Please help as the conception is not clear to me.
And one more thing is that the traj file is look like:
# step distanceZ
           0 7.87607744204158e+01
         200 7.31112828886414e+01
         400 6.71194308765552e+01
         600 6.29314331811324e+01
         800 5.97378222403360e+01
        1000 5.62958276760813e+01

My question is that what is the meaning of distanceZ, is it the
distance between the two selected atoms? Then by what rule it
decreases, as the decrease is not same.
 Any type of suggestions will be really helpful to me. Please help.

Ipsita Basu
Research Fellow
c/o : Dr. Chaitali Mukhopadhyay
Rajabazar Science College
92 APC Road
Kolkata - 700009

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