On Sat, Nov 9, 2013 at 9:36 AM, alex.bjorling <alex.bjorl...@gmail.com>wrote:
> Dear users, > > I am investigating protein crystal packing artifacts by doing equilibrium > simulations starting from a crystal structure. I would like to know if the > relaxations i see are reproducible, in the sense that many simulations with > independent velocities give the same general result. > > My plans is to do only one set of (first NVT then NPT) equilibrations with > position restraints. Then, I thought I'd do a shorter NPT run with position > restraints, with more frequent output and using the trr snapshots as > starting points for production runs. > > The only question then is how far apart these snapshots need to be to > guarantee independent velocities. Attached is the velocity autocorrelation > for the Protein group. It seems to me that using snapshots 1ps apart would > do it, since the autocorrelation has decayed by then. > > Is this a valid approach? > That the observations are uncorrelated (because the autocorrelation time has elapsed) does not imply that trajectories started from successive snapshots would be independent - in the absence of floating-point or load-balancing artefacts leading to numerical divergence, the separate simulations would nearly reproduce each other! Since you have to wait for a period of divergence anyway, you might as well generate new velocities after an initial stage of equilibration, equilibrate further, and have no independence question to answer. Mark -- 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
