umbrella sampling

From: ipsita basu (
Date: Wed Jul 11 2012 - 06:48:16 CDT

 I want to umbrella sampling in my membrane protein simulation to
calculate potential mean force. My colvar configuration file is:
colvarsTrajFrequency 200
colvar {
  name length
  distance {
    group1 {
      atomNumbersRange 94313-98031
    group2 {
      atomNumbers 1503 2307 2709
harmonic {
  name lenpot
  colvars length
  centers 17.0
  forceConstant 1.0
  targetCenters 80.0
  targetNumSteps 400

I want to vary the z-distance between group 1 and group 2.
I put the initial zav value of group 1 in centers (centers 17.0)
and the zav value of group in targetCenters.
Now I am just a beginner in umbrella sampling and I've some queries
about this. My questions are:
1. Is that right what I'm doing or I misunderstood?
2. What should be the value of targetNumsteps? Is it should be the
value during which the distance will reduce by the given width?
3. should the rest system will be position restrained?

Any type of help will be really appreciated.
If the questions are bizarre then I'm sorry.

Thanking you,
Yours faithfully

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

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