[gmx-users] analysis of POPC
anoddlad at yahoo.com
Sat Feb 2 14:08:26 CET 2008
You'd have thought the MD papers you have would also compare values against experimental data?
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.
In summary, try harder ;)
----- Original Message ----
From: pragya chohan <pragyachohan at hotmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Saturday, February 2, 2008 12:54:35 PM
Subject: RE: [gmx-users] analysis of POPC
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.
If anyone happens to have such papers please send them to me at pragyachohan at hotmail.com.
> Date: Sat, 2 Feb 2008 07:20:54 -0500
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] analysis of POPC
> Quoting pragya chohan <pragyachohan at hotmail.com>:
> > hello users
> > I am trying to do analysis after bilayer simulation. I cannot get any
> > experimental data on POPC to validate my model with. Can the people who are
> > working on same lipid tell me some references and also what analysis should
> > be done of the bilayer before putting protein into it?
> I spent less than two minutes on Google and found papers giving all sorts of
> experimental parameters (density, area per headgroup, bilayer thickness, etc).
> I suggest you try the same.
> In terms of the analysis you need to do, that is up to what question you are
> asking and why you are simulating this particular lipid. Refer to the
> literature and find papers by groups that have simulated proteins in POPC (and
> perhaps proteins in membranes in general) to determine what they have found
> relevant, and apply the same to your system.
> > _________________________________________________________________
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> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul at vt.edu | (540) 231-9080
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