Hello Michael, I believe a non-parallel implementation is fine. Thank you for the guidance.
I am running QM/MM calculations in GROMACS over relatively short timescales (10 ps) with a fine timestep (0.1 fs). My system follows the dynamics of atoms with thermal and hyperthermal velocities and the literature suggests that second order methods can become numerically unstable during collision events. These publications recommend a predictor/corrector integrator. Best, Eric On Tue, Aug 11, 2015 at 12:04 PM, Michael Shirts <mrshi...@gmail.com> wrote: > Adding an integrator for your own work is hard but doable, especially > if you don't need it parallelized. Look at the do_update_X routines > for examples. It will be harder for 5th/6th order since you probably > need values of the forces for times in the past, which are not > automatically stored in gromacs -- you'll have to add arrays to store > them yourself (which will get rather hard with parallelization). > > Adding something that other people could use as a general release -- > probably not something you would want to try now. Some plans in the > works to make it easier, but it will be a few months at the soonest. > > Just wondering about adding predictor/corrector integrators. They > tend to be quite bad over longer time scales. Is there a particular > reason? > > On Tue, Aug 11, 2015 at 1:24 PM, Eric Smoll <ericsm...@gmail.com> wrote: > > Hello GROMACS users, > > > > I am interested in adding a fifth/sixth order predictor/corrector > > integrator to GROMACS. Is this possible? If so, any guidance on which > files > > need to be updated is much appreciated. > > > > Best, > > Eric > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
