Hi ALL, Thanks a lot for the replies. By long simulation I mean 500 ns to 1000 ns. Has anybody tried with the ff43a1 with any membrane protein?
Thanks, Anirban On Fri, Apr 20, 2012 at 3:26 AM, Peter C. Lai <p...@uab.edu> wrote: > Define long simulations? CHARMM27/36 in the sub-100ns timescale works for > us. > > The following paper: > Vanni, S., Neri, M., Tavernelli, I., and Rothlisberger, U.: Predicting > Novel Binding Modes of > Agonists to Adrenergic Receptors Using All-Atom Molecular Dynamics > Simulations. PLoS > Comput Biol 7, e1001053 (2011) > > Uses Amber99SB over 500-800+ns for their beta2-adrenergic receptor system. > > On 2012-04-19 12:02:36PM +0530, Anirban Ghosh wrote: > > Hi ALL, > > > > When running a membrane protein (say GPCR) in a lipid bilayer (say POPC > or > > DPPC etc.) which according to your experience is the most suited > > force-field in GROMACS that best retains the 7TM / secondary structures > of > > the protein over long simulations? I have tried running with ff53a6 (as > > suggested in Justin's tutorial), but find that the helices in the bilayer > > tend to lose their helicity over time and turns into coils. ff43a2 seems > to > > do the job somewhat better by retaining the helicity. Will ff43a1 work > even > > better as the principle aim is to observe changes in the protein without > > losing its secondary structures? Your experience please. > > Thanks a lot in advance. > > > > > > Regards, > > > > Anirban > > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > ================================================================== > Peter C. Lai | University of Alabama-Birmingham > Programmer/Analyst | KAUL 752A > Genetics, Div. of Research | 705 South 20th Street > p...@uab.edu | Birmingham AL 35294-4461 > (205) 690-0808 | > ================================================================== > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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