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? Best, Alex <http://gromacs.5086.x6.nabble.com/file/n5012372/vac.png> -- View this message in context: http://gromacs.5086.x6.nabble.com/Reproducing-results-with-independent-runs-tp5012372.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list firstname.lastname@example.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