David van der Spoel wrote: > patrick fuchs wrote: >> Hi David, >> since updated GROMOS force fields are now available within GROMACS, I >> agree one does not need to use ffgmx, at least for standard simulations. >> The only problem is for lipid/protein simulations. The only publicly >> available I know that runs under GROMACS is the combination of Berger >> lipids with ffgmx (on the website of Peter Tieleman). For someone >> starting a project of lipid/protein simulations, there is a priori no >> other public alternative (using GROMACS), although I know some new >> parameters are about to be published. >> Cheers, > > But the Berger et al force field is based upon OPLS, and hence it can > be combined with OPLS all atom FF. > These parameters were developed with united-atom OPLS. Tieleman and co-workers introduced modifications to allow the usage of these parameters with all atom OPLS (Tieleman et al., J. Phys. Condens. Matter 18 S1221-34, 2006). I would use it with cautious though, the results show significant differences between ffgmx and OPLSAA (Table 1 of the paper above). In addition, there can be an error in the range of 10 kCal/mol in the calculated cyclohexane to water transfer energies with OPLS (in any combination, Table 3 of Tieleman et al.). I found this alarming, but haven't seen results from other FFs - the error may be just as big.
Ran. _______________________________________________ gmx-users mailing list [email protected] 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
