Re: [gmx-users] membrane with OPLS force field

Volker Wirth wrote: Hi Justin, thanks a lot for your response! Of course my mail was a bit "provocative", as I know that combination methods are state of the art, used in many publications and leading to reasonable results. (time scale eight months). Combining different force fields (Berger/

Re: [gmx-users] membrane with OPLS force field

Hi Justin, thanks a lot for your response! Of course my mail was a bit "provocative", as I know that combination methods are state of the art, used in many publications and leading to reasonable results. >> (time scale eight months). Combining different force fields >> (Berger/GROMOS, Berger/OPLS

Re: [gmx-users] membrane with OPLS force field

Volker Wirth wrote: standard acyl chain parameters fail when they get too long. I think there ref. for that is a Berendsen paper on hexadecane simulations, but I could be wrong there. In any event, 'protein' parameters do not appear to transfer directly to long acyl chains in a simple way and t

Re: [gmx-users] membrane with OPLS force field

> standard acyl chain parameters fail when they get too long. I think there > ref. for that is a Berendsen paper on hexadecane simulations, but I could be > wrong there. In any event, 'protein' parameters do not appear to > transfer directly to long acyl chains in a simple way and therefore your >

[gmx-users] membrane with OPLS force field

Sorry for my misunderstanding. You can not use standard OPLS parameters for lipids. Even if you go through the paramaterization process (see the gromace wiki and the original OPLS papers) then you are still stuck with the fact that standard acyl chain parameters fail when they get too long. I

RE: [gmx-users] membrane with OPLS force field

; 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

[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

Re: [gmx-users] membrane with OPLS force field

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 kno

[gmx-users] membrane with OPLS force field

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