# Re: umbrella sampling

From: koushik.k (koushik.k_at_students.iiit.ac.in)
Date: Tue Jun 26 2012 - 03:19:23 CDT

Dear Ipsita,

Look through the NAMD mailinglist archives. There have been numerous
discussions on umbrella sampling and its implementation in NAMD using
colvars module. Please go through them and you will find all the
information you need.

Koushik Kasavajhala
Master of Science by Research in Bioinformatics
Center for Computational Natural Sciences and Bioinformatics (CCNSB)
International Institute of Information Technology, Hyderabad (IIIT-H)
India

On Tue, 26 Jun 2012 10:43:18 +0530, ipsita basu wrote:
> Thank you very much sir for your reply.
> Yes I want to do umbrella sampling. But in the given tutorial
> umbrella
> sampling is not specifically mentioned. Should I follow "Harmonic
> restraints and Steered Molecular Dynamics" this section or
> "Implementation of the free energy methods in NAMD" as free energy
> can be calculated from the both.
>
> On 6/25/12, Giacomo Fiorin <giacomo.fiorin_at_gmail.com> wrote:
>> 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 outdated.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
>>
>> 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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