Generating velocities from a new random seed is normally regarded as good enough. By the time you equilibrate, the chaotic nature of MD starts to work for you.
Mark On Nov 21, 2012 1:04 PM, "Felipe Pineda, PhD" <luis.pinedadecas...@lnu.se> wrote: > So how would you repeat the (let be it converged) simulation from > different starting conditions in order to add that valuable statistics you > mention? > > I think this was Albert's question > > Felipe > > On 11/21/2012 12:41 PM, Mark Abraham wrote: > >> If a simulation ensemble doesn't converge reliably over a given time >> scale, >> then it's not converged over that time scale. Repeating it from different >> starting conditions still adds valuable statistics, but can't be a >> replicate. Independent replicated observations of the same phenomenon >> allow >> you to assess how likely it is that your set of observations reflect the >> underlying phenomenon. The problem in sampling-dependent MD is usually in >> making an observation (equating a converged simulation with an >> observation). >> >> Mark >> >> On Wed, Nov 21, 2012 at 8:12 AM, Albert <mailmd2...@gmail.com> wrote: >> >> hello: >>> >>> I am quite confused on how to repeat our MD in Gromacs. If we started >>> from the same equilibrated .gro file with "gen_vel = no" in >>> md.mdp, >>> we may get "exactly" the same results which cannot be treated as >>> reasonable >>> repeated running. However, if we use "gen_vel=yes" for each round of >>> running, sometimes our simulation may not converged at our simulated time >>> scale and we may get two results with large differences. >>> >>> So I am just wondering how to perform repeated MD in Gromacs in a >>> correct way so that our results can be acceptably repeated? >>> >>> thank you very much. >>> Albert >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users> >>> <htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> > >>> * Please search the archive at http://www.gromacs.org/** >>> Support/Mailing_Lists/Search<h**ttp://www.gromacs.org/Support/** >>> Mailing_Lists/Search<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<http://www.gromacs.org/**Support/Mailing_Lists> >>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> > >>> >>> > > -- > +-----------------------------**------+ > | Luis Felipe Pineda De Castro, PhD | > | Computational Chemist - Postdoc | > | Computational Chemistry and | > | Biochemistry Laboratory | > | School of Natural Sciences | > | Linnaeus University | > | SE-391 82 Kalmar | > | Norrgård, room 311 | > | Sweden - Sverige | > | Phone: ++46-480-44 6329 | > | Mobile: ++46-76-8420572 | > | E-Mail: luis.pinedadecas...@lnu.se| > | Web: lnu.se | > +-----------------------------**------+ > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- 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
