David van der Spoel ha scritto: > On 2/2/10 4:43 PM, ms wrote: >> David van der Spoel ha scritto: >> >>> On 2/1/10 4:32 PM, ms wrote: >>> >>>> Hi, >>>> >>>> Sorry for the offtopic but Google/literature quick search is not >>>> helping >>>> and I'd like to have some more informed opinion. >>>> >>>> To my understanding, GROMACS isn't capable of discontinuous molecular >>>> dynamics. Is there any more-or-less standard software package for that? >>>> >>>> thank you! >>>> m. >>>> >>> Can you be more specific please? >>> >>> >> Uhm, in what meaning? >> I was pondering about using DMD for use with a coarse-grained model and >> I wondered if there is a standard package for that. Don't know how to be >> more specific, what is unclear in my question? >> >> thanks, >> M. >> > What is discrete MD?
Uh, sorry. Probably references know better than me: http://pubs.acs.org/doi/full/10.1021/ja0539140 is an example of it applied to proteins. (I am looking for reviews on the subject but can't find recent ones) It is a coarse-grained technique for use with discontinuous potentials, which roughly speaking uses "collision detection" instead of fine-grained potential calculation: "In a discontinuous molecular dynamics (DMD) simulation, particles collide when they arrive at a discontinuity in the potential, that is, the hard-sphere diameter or the square-well width. Between collisions, particles move with linear trajectories, making DMD simulations much faster than traditional molecular dynamics simulations with continuous potentials which require a small integration time step. The postcollision velocities of particles in DMD are found by solving the collision dynamics equations analytically." (from http://pubs.acs.org/doi/full/10.1021/la049267s ) I don't know much about it, but I was curious and I wanted to know if there was a package for it (or if Gromacs was capable of it). thanks! m. -- gmx-users mailing list [email protected] http://lists.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
