<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><br><br>--- On <b>Mon, 3/8/09, Justin A. Lemkul <i><jalemkul@vt.edu></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: Justin A. Lemkul <jalemkul@vt.edu><br>Subject: Re: [gmx-users] analysis of result<br>To: "Gromacs Users' List" <gmx-users@gromacs.org><br>Date: Monday, 3 August, 2009, 8:23 PM<br><br><div class="plainMail"><br><br>Samik Bhattacharya wrote:<br>> <br>> <br>> --- On *Mon, 3/8/09, Justin A. Lemkul /<<a ymailto="mailto:jalemkul@vt.edu" href="/mc/compose?to=jalemkul@vt.edu">jalemkul@vt.edu</a>>/* wrote:<br>> <br>> <br>> From: Justin A. Lemkul <<a ymailto="mailto:jalemkul@vt.edu" href="/mc/compose?to=jalemkul@vt.edu">jalemkul@vt.edu</a>><br>> Subject: Re: [gmx-users] analysis of
result<br>> To: "Discussion list for GROMACS users" <<a ymailto="mailto:gmx-users@gromacs.org" href="/mc/compose?to=gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> Date: Monday, 3 August, 2009, 5:03 PM<br>> <br>> <br>> <br>> Samik Bhattacharya wrote:<br>> > hi i have completed the process of simulating a protein in a<br>> lipid environmant... now in the analysis part i have generated some<br>> graphical representations of the angle, RMSD etc. but from that i<br>> cant conclude about the success of the simulation.....is there any<br>> thing (research papers, namely) whcih can provide ideas about how to<br>> reach conclusion from the analysed data.....really need some help<br>>
regarding this matter....<br>> <br>> Everyone's conclusions are going to be different based on the<br>> question they are trying to answer. The necessary analysis should<br>> be derived from this question. Such decisions should be made before<br>> running the MD :)<br>> <br>> -Justin<br>> <br>> > Thank You<br>> > Shamik<br>> <br>> <br>> first of all thanks a lot Justin for your reply.....obviously i<br>> agree with you. i want to study the activity of some membrane<br>> proteins in different environments. for that i just want to know<br>> which parameters i need to consider. things which are common has<br>>
already been analyzed....i just need some references to make sure<br>> i'm not missing any details which could lead me to any other<br>> conclusion...<br><br>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 :)<br><br>-Justin<br><br>> waiting for you reply..<br>> Thanks a lot for your time and really helpful suggestions....<br>> <br>> Shamik<br>> <br>><span style="text-decoration: underline;"><br>
</span>ok, thank you Justin....i got what you meant to say.... thanks you for the help...<br>
Shamik<br>
<span style="text-decoration: underline;"></span></div></blockquote></td></tr></table><br>
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