Dear all, I am still interested in some integrator related issues.
I understand that the easiest way to implement velocity Verlet was to split the updates in two updates. But I don't understad the order of those updates. I mean why there are two updates for velocities and then the update for positions? My intuitive idea would be to update first one half for velocities, then a full step for positions and, finally, using these new positions the second half for velocities. Maybe I am missunderstanding something. Thank you very much, Mario Fernández-Pendás 2014-03-23 14:33 GMT+01:00 Michael Shirts <mrshi...@gmail.com>: > Putting both velocity Verlet and leapfrog Verlet both in Gromacs turns > out to be non-trivial for the bookkeeping. The easiest way to do this > was split the velocity Verlet updates. > > Also, the additional computational cost of two half steps for > velocities is trivial compared to the cost of the forces for almost > all systems. > > On Sun, Mar 23, 2014 at 8:39 AM, Mario Fernández Pendás > <mariof...@gmail.com> wrote: > > Dear all, > > > > In terms of computational efficiency, why the velocity Verlet integrator > is > > implemented in GROMACS in one full step for positions and two half steps > > for velocities? > > > > Would it be more efficient to merge the second halft step for velocities > > with the first half step of the following scheme, ie, integrating in one > > full step for velocities? > > > > Thank you very much, > > Mario Fernánez-Pendás > > -- > > 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.
