<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">You'd have thought the MD papers you have would also compare values against experimental data?</DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">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.</DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">In summary, try harder ;)<BR><BR></DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">----- 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>
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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" target=_blank rel=nofollow ymailto="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>> > _________________________________________________________________<BR>> > Tried the new MSN Messenger? It¢s cool! Download now.<BR>> > <A href="http://messenger.msn.com/Download/Default.aspx?mkt=en-in"
target=_blank>http://messenger.msn.com/Download/Default.aspx?mkt=en-in</A><BR>> <BR>> <BR>> <BR>> ========================================<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>> <A href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/" target=_blank>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/</A><BR>> <BR>> ========================================<BR>> _______________________________________________<BR>> gmx-users mailing list gmx-users@gromacs.org<BR>> <A href="http://www.gromacs.org/mailman/listinfo/gmx-users" target=_blank>http://www.gromacs.org/mailman/listinfo/gmx-users</A><BR>> Please search the archive at <A href="http://www.gromacs.org/search" target=_blank>http://www.gromacs.org/search</A> before posting!<BR>> Please don't post
(un)subscribe requests to the list. Use the <BR>> www interface or send it to gmx-users-request@gromacs.org.<BR>> Can't post? Read <A href="http://www.gromacs.org/mailing_lists/users.php" target=_blank>http://www.gromacs.org/mailing_lists/users.php</A><BR><BR><BR>
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