[gmx-users] membrane with OPLS force field
Rebeca García Fandiño
regafan at hotmail.com
Tue Aug 5 15:47:57 CEST 2008
Ok, thank you very much. However, with this combination I am not using all atoms for the lipds, if I am right and my intention was using all atoms both for the protein and the membrane.
Thank you very much for your help.
Rebeca García.> Date: Tue, 5 Aug 2008 09:44:17 -0400> From: chris.neale at utoronto.ca> To: gmx-users at gromacs.org> Subject: [gmx-users] membrane with OPLS force field> > There is no such thing as an OPLS bilayer. The method that was specified to combine the opls-PROTEIN and berger-LIPIDS is currently the only way that one can do this combination exactly. What this means, is that if you simulate a bilayer using the files downloaded from Peter Tieleman's website then you get exactly the same thing as when you use the mentioned combination rules for "OPLS" (in cases where you do not have a protein). For the proof, see here:> > http://www.pomeslab.com/files/lipidCombinationRules.pdf> > (although our server appears to be down right now, you might check back near the end of the day today).> > Once you add a protein, however, everything is expected to change, and it has in fact not yet been proven that this combination is without bias. In fact, it will certainly have some bias! However, given the available options I believe that this is currently the best available combination. If the charmm parameters were included in the standard gromacs distribution and somebody else had already tested the lipid properties of that distribution, then I might change my mind. > > Chris.> > -- original message --> > Rebeca García Fandiño wrote:> > > > Hello,> > > I would like to simulate a membrane + protein system using the OPLS > > > force field for both, the protein and the membrane. I have looked for a > > > previous equilibrated membrane simulated using the OPLS force field, but > > > I did not find it.> > > Please, does anybody knows where I could find a membrane simulated with > > > the OPLS force field?> > > > I've never seen one either. The Berger parameters (commonly used) are based in > part on OPLS parameters, and as such, Chris Neale has posted a nice procedure > for modifying the Berger parameters (present at Tieleman's site as lipid.itp) > such that they can be used in conjunction with an OPLS representation of your > protein:> > http://www.gromacs.org/pipermail/gmx-users/2006-May/021416.html> > Recent literature (from Tieleman's group) has suggested that this is a more > accurate representation of protein-lipid interactions than the classic > Gromos+Berger representation that is quite common in the literature.> > If you're desperate for an OPLS bilayer, you may have to generate it yourself.> > _______________________________________________> gmx-users mailing list gmx-users at gromacs.org> http://www.gromacs.org/mailman/listinfo/gmx-users> Please search the archive at http://www.gromacs.org/search before posting!> Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-request at gromacs.org.> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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