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.
At 07:08 AM 2/2/2008, Alan Dodd wrote:
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 <[email protected]>
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 <mailto:[EMAIL PROTECTED]>[EMAIL PROTECTED]
> Date: Sat, 2 Feb 2008 07:20:54 -0500
> From: [EMAIL PROTECTED]
> To: [email protected]
> 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.
> >
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>
>
> ========================================
>
> 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/>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>
> ========================================
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