[gmx-users] analysis of result

Samik Bhattacharya samikbhat at yahoo.co.in
Tue Aug 4 03:31:34 CEST 2009

--- 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: "Gromacs Users' List" <gmx-users at gromacs.org>
Date: Monday, 3 August, 2009, 8:23 PM

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...

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 :)


>     waiting for you reply..
>     Thanks a lot for your time and really helpful suggestions....
>     Shamik

  ok, thank you Justin....i got what you meant to say.... thanks you for the help...



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