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There are fewer data for POPC than for DOPC and DPPC. If your force
fields and methods give you good results for DOPC and DPPC, you should be
in good shape for POPC, since the building blocks are the same, but just
rearranged.<br><br>
At 07:08 AM 2/2/2008, Alan Dodd wrote:<br>
<blockquote type=cite class=cite cite="">You'd have thought the MD papers
you have would also compare values against experimental data?<br>
These papers do exist, I'm sure, I came across the all the time while
looking for DOPC data - though I didn't make a note of them. Plus
the people who initially parameterised the POPC topology (Tieleman?) must
have compared results to experimental data.<br>
In summary, try harder ;)<br><br>
----- Original Message ----<br>
From: pragya chohan <pragyachohan@hotmail.com><br>
To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>
Sent: Saturday, February 2, 2008 12:54:35 PM<br>
Subject: RE: [gmx-users] analysis of POPC<br><br>
Thanks, but I did get some papers on the analysis done on POPC by MD but
I did not get any experimental papers showing the values so that I can
compare results of my MD with experimental data.<br>
If anyone happens to have such papers please send them to me at
<a href="mailto:pragyachohan@hotmail.com">pragyachohan@hotmail.com</a>
.<br>
> Date: Sat, 2 Feb 2008 07:20:54 -0500<br>
> From: jalemkul@vt.edu<br>
> To: gmx-users@gromacs.org<br>
> Subject: Re: [gmx-users] analysis of POPC<br>
> <br>
> Quoting pragya chohan <pragyachohan@hotmail.com>:<br>
> <br>
> ><br>
> > hello users<br>
> > I am trying to do analysis after bilayer simulation. I cannot
get any<br>
> > experimental data on POPC to validate my model with. Can the
people who are<br>
> > working on same lipid tell me some references and also what
analysis should<br>
> > be done of the bilayer before putting protein into it?<br>
> <br>
> I spent less than two minutes on Google and found papers giving all
sorts of<br>
> experimental parameters (density, area per headgroup, bilayer
thickness, etc). <br>
> I suggest you try the same.<br>
> <br>
> In terms of the analysis you need to do, that is up to what question
you are<br>
> asking and why you are simulating this particular lipid. Refer to
the<br>
> literature and find papers by groups that have simulated proteins in
POPC (and<br>
> perhaps proteins in membranes in general) to determine what they
have found<br>
> relevant, and apply the same to your system.<br>
> <br>
> -Justin<br>
> <br>
> >
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> ========================================<br>
> <br>
> Justin A. Lemkul<br>
> Graduate Research Assistant<br>
> Department of Biochemistry<br>
> Virginia Tech<br>
> Blacksburg, VA<br>
> jalemkul@vt.edu | (540) 231-9080<br>
>
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---------------------------------<br>
Eric Jakobsson, Ph.D.<br>
Professor, Department of Molecular and Integrative Physiology, and of
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