[gmx-users] analysis of result

[Justin A. Lemkul]

Samik Bhattacharya wrote:
> 
> 
> --- On *Mon, 3/8/09, Justin A. Lemkul /<jalemkul at vt.edu>/* wrote:
> 
> 
>     From: Justin A. Lemkul <jalemkul at vt.edu>
>     Subject: Re: [gmx-users] analysis of result
>     To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>     Date: Monday, 3 August, 2009, 5:03 PM
> 
> 
> 
>     Samik Bhattacharya wrote:
>      > hi i have completed the process of simulating a protein in a
>     lipid environmant... now in the analysis part i have generated some
>     graphical representations of the angle, RMSD etc. but from that i
>     cant conclude about the success of the simulation.....is there any
>     thing (research papers, namely) whcih can provide ideas about how to
>     reach conclusion from the analysed data.....really need some help
>     regarding this matter....
> 
>     Everyone's conclusions are going to be different based on the
>     question they are trying to answer.  The necessary analysis should
>     be derived from this question.  Such decisions should be made before
>     running the MD :)
> 
>     -Justin
> 
>      > Thank You
>      > Shamik
> 
> 
>     first of all thanks a lot Justin for your reply.....obviously i
>     agree with you. i want to study the activity of some membrane
>     proteins in different environments. for that i just want to know
>     which parameters i need to consider. things which are common has
>     already been analyzed....i just need some references to make sure
>     i'm not missing any details which could lead me to any other
>     conclusion...

A simple literature search will turn up dozens (if not hundreds) of useful 
papers related to membrane protein MD.  There are not necessarily any universal 
parameters that should be analyzed - if your study is about activity of a 
membrane protein, is lateral diffusion of lipids important?  If the answer is 
no, then you've wasted your time running the analysis and searching for papers 
about it :)

-Justin

>     waiting for you reply..
>     Thanks a lot for your time and really helpful suggestions....
> 
>     Shamik
> 
> 
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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