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.
Best wishes,
Rebeca García.> Date: Tue, 5 Aug 2008 09:44:17 -0400> From: [EMAIL PROTECTED]>
To: gmx-users@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@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 [EMAIL PROTECTED]> Can't post? Read
http://www.gromacs.org/mailing_lists/users.php
_________________________________________________________________
¡Lo mejor de MSN y Windows Live en tu móvil! Hotmail, Messenger, Spaces…
Pruébalo ya y disfruta de todas sus ventajas donde quieras
http://serviciosmoviles.es.msn.com/
_______________________________________________
gmx-users mailing list gmx-users@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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
