how long were those simulations? Were there enough time for the new ensemble to equilibrate, if you changed ensemble from NVE to NVT?
On Sun, Oct 19, 2014 at 11:34 AM, Wade <wad...@foxmail.com> wrote: > Dear Mark and Lu, > Thank you very much for your responses. > Based on your suggestions, I performed some tests: > 1) I considered the influence of the time-step (with LINCS constraint), > thermostat, and simulation precision in NVT simulation > (tip4p water box, 300K, after 2ns NVE simulation). > Below are results: > ----------- > Time-step (fs) thermostat (V or N) precision (S or D) > drift/ns = delt E/av E*100% > 0.1 V D 0.3 > 1 V D 2 > 2 V D 5.8 > > > 0.1 V S 80 > 1 V S 1.5 > 2 V S 6.4 > > > 0.1 N D 0.3 > 1 N D 2.5 > 2 N D 20 > > > 0.1 N S 76 > 1 N S 1.7 > 2 N S 11.5 > ------------------ > Above results shown that no matter the v-rescale or nose-hoover > thermostat, the conserved Energy has nearly no drift (~0.3%/ns) > when an very small time-step (0.1 fs) has been employed. But, even with > 0.1fs step length, the integration can only be conserved in > the double precision simulations. > For a commonly used time-step, such as 2 fs (with LINCS constraint), the > drifts of the conserved energy are about 6-7% per ns. > Such a drift might be not very significant in a short simulation. But, its > accumulation in a long-time (e.g. several ns) simulation should be huge. > > > 2) I checked the time-dependency of auxiliary dynamics purely, and found > that it was the origination of the constant-rate drift of conserved energy. > I also noticed that the exact solution of Eq.7 in bussi’s paper (Eq. A7) > has been realized in gromacs to get the rescaling factor. > But, I don’t know what the origination of the integration error is, and > How can we deal with it. > As Lu said, does it comes from the summation of dK? If yes, how can we > deal with the drift when we use an affordable time-step in a long-time > simulation? > > > With best wishes, > > > Wade > > -- > 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.
