From: ipsita basu (ibasu788_at_gmail.com)
Date: Tue Jun 26 2012 - 00:13:18 CDT
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 Hello Ipsita, the questions are not ridiculous, but certainly outdated.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
> 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
>>
>>
>
-- Ipsita Basu Research Fellow c/o : Dr. Chaitali Mukhopadhyay Rajabazar Science College 92 APC Road Kolkata - 700009
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