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 <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users <gmx-users@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 [EMAIL
PROTECTED]
> Date: Sat, 2 Feb 2008 07:20:54 -0500
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] analysis of POPC
>
> Quoting pragya chohan <[EMAIL PROTECTED]>:
>
> >
> > 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.
>
> -Justin
>
> > _________________________________________________________________
> > Tried the new MSN Messenger? It’s cool! Download now.
> > http://messenger.msn.com/Download/Default.aspx?mkt=en-in
>
>
>
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> [EMAIL PROTECTED] | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>
> ========================================
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