From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Jun 25 2012 - 09:15:50 CDT
Hello Ipsita, the questions are not ridiculous, but certainly outdated.
The input is for an older implementation of the ABF method, which has been
replaced by the one in the collective variables module. Go to the user's
guide and read the section for ABF:
http://www.ks.uiuc.edu/Research/namd/current/ug/
Second, ABF is not umbrella sampling, they are two completely separate
methods. If you wanted to do umbrella sampling, read the corresponding
section instead.
Third, A(xi) in the output was the free energy as a function of the
collective variable, or reaction coordinate xi. The choice of what
variable to use is by far the most important part of a free energy
calculation. If you're not sure what to use, I couldn't discourage more
strongly from using someone else's script.
Bests
Giacomo
On Mon, Jun 25, 2012 at 3:22 AM, ipsita basu <ibasu788_at_gmail.com> wrote:
> Sir,
> 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
> (http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/7378.html).
> 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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