[gmx-users] analysis of POPC

[Eric Jakobsson]

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 <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 <mailto:pragyachohan at hotmail.com>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.
> >
> > -Justin
> >
> > > _________________________________________________________________
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> >
> >
> > ========================================
> >
> > Justin A. Lemkul
> > Graduate Research Assistant
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul at vt.edu | (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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---------------------------------
Eric Jakobsson, Ph.D.
Professor, Department of Molecular and 
Integrative Physiology, and of Biochemistry, and 
of the Center for Biophysics and Computational Biology
Senior Research Scientist, National Center for Supercomputing Applications
Professor, Beckman Institute for Advanced Science and Technology
3261 Beckman Institute, mc251
University of Illinois, Urbana, IL 61801
ph. 217-244-2896  Fax 217 244 9757



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