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--- Dr. Vlad Cojocaru Max Planck Institute Muenster Roentgenstrasse 20, 48149 Muenster, Germany Tel: +49-251-70365324 Sent from my mobile phone; Sorry for being short and for any errors Albert <mailmd2011.gmail.com> wrote: >From the link J B gave, they run 400/500 ns for each lipids, it seems to be good. probably we can just read the paper J B mentioned to see how it well for protein/membrane system. Albert On 06/22/2012 07:45 AM, Vlad Cojocaru wrote: > I saw these on a poster at a recent conference. I did not read the paper but from the poster I understood that they are very much based on charmm36. Unfortunately I could not speak with the author. > > I would like to say that people should be cautious when deciding if 2 force fields are cmpatible. A qualitative agreement is not enough. A quatitative reproduction of experinentally derived energies is required. > > All I want to say is that those who would like to use these parameters for protein-membrane (with amber proteins) simulations should carefully assess the combatibility issue before running massess of simulations. > > Vlad > --- > Dr. Vlad Cojocaru > Max Planck Institute Muenster > Roentgenstrasse 20, > 48149 Muenster, Germany > Tel: +49-251-70365324 > > Sent from my mobile phone; Sorry for being short and for any errors > > J B <john.b.86.hotmail.com> wrote: > > > I am a Gromacs user and I have tried these parameters that are supposed to be compatible with the AMBER force fields: > http://web.me.com/jambeck/lipids/Downloads.html > And they work well for saturated PC lipids without applying a surface tension and apparently parameters for unsaturated lipids are on the way. > Used a real space cut off of 10 angstrom and a LJ cut off of 12 Angstrom and got good results compared to experiments. > I guess that these parameters are easy to use in AMBER... >_____________________________________________ > > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > >_____________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _____________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Thu Jun 21 2012 - 23:00:04 PDT