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
