On Nov 11, 2010, at 6:35 PM, George Khelashvili wrote: > I am relatively new to Martini force fields and the fact that masses of all > the coarse grained beads are set to a same value (72amu) somewhat bothers me. > I was wondering what influence may this have on the process of spontaneous > lipid aggregation into different phases? I read that it will generally > influence the kinetics of the process, but how about the actual final outcome?
As long as by "final outcome" you mean equilibrium properties, you don't have to worry about masses too much. Masses usually appear only in the kinetic energy part of the energy function, which decouples from the configurational part of the Boltzmann weight. Of course, if you study a system where the masses couple to positional degrees of freedom (e.g., gravity), you have to be more careful. > Should I expect that the correct phase of lipid/water mixture will be formed > in the appropriate region of the phase space using default parameters? I haven't used the Martini force field, but like all other force fields I would expect it to work well only for those situations for which it has been parametrized. Everything beyond that would require careful validation. Hope this helps, Lutz -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
