[gmx-users] analysis of result

Samik Bhattacharya samikbhat at yahoo.co.in
Mon Aug 3 16:19:19 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: "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 :)


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


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