umbrella sampling

From: ipsita basu (
Date: Mon Jun 25 2012 - 02:22:21 CDT

I want to do umbrella sampling on my membrane protein system. I want
to divide the windows on the basis of the z axis distance between the
protein centre of mass and that of the membrane. I followed the script
My abf portion is given below:
abf coordinate distance
abf abf1 3719
abf abf2 19028
abf dxi 0.1
abf xiMin 36.74
abf xiMax 66.74
abf outFile da-1.abf.dat
abf fullSamples 500
abf inFiles {}
abf distFile da-1.abf.dist
abf dSmooth 0.0
abf restraintList {
        dist1 {dist {A 1 N} {A 194 CA} 1.0 9.23}

My questions are:
1) In abf1 I give the total no of atoms participating in forming the
centre of mass of the protein and for abf2 I give the same for the
membrne. So am I right?
2) Should the protein should be position restrained in each window?
Then how to fix it?
3) The output dat file is look like:
# xi A(xi) av_force n_samples
      36.790 0.0000 -1.7136 382
      36.890 0.2375 -3.0363 408
What is the A(xi)? Is it the position of the COM of the protein?
Any help from your end will be appreciated.
If the questions are ridiculous then I'm sorry.

Thanking you,
Ipsita Basu

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

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