--- On Mon, 3/8/09, Justin A. Lemkul <jalem...@vt.edu> wrote:
From: Justin A. Lemkul <jalem...@vt.edu>
Subject: Re: [gmx-users] analysis of result
To: "Gromacs Users' List" <gmx-users@gromacs.org>
Date: Monday, 3 August, 2009, 8:23 PM
Samik Bhattacharya wrote:
>
>
> --- On *Mon, 3/8/09, Justin A. Lemkul /<jalem...@vt.edu>/* wrote:
>
>
> From: Justin A. Lemkul <jalem...@vt.edu>
> Subject: Re: [gmx-users] analysis of result
> To: "Discussion list for GROMACS users" <gmx-users@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
>
>
ok, thank you Justin....i got what you meant to say.... thanks you for the
help...
Shamik
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