Samik Bhattacharya wrote:
--- On *Mon, 3/8/09, Justin A. Lemkul /<[email protected]>/* wrote:
From: Justin A. Lemkul <[email protected]>
Subject: Re: [gmx-users] analysis of result
To: "Discussion list for GROMACS users" <[email protected]>
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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--
========================================
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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