But is the effect of varying ld_seed.. can that make different trajectories stochastic?
On Wed, Sep 21, 2011 at 7:40 PM, Mark Abraham <mark.abra...@anu.edu.au> wrote: > On 22/09/2011 6:21 AM, Sai Pooja wrote: >> >> Hi, >> >> The sd integrator is described in the manual as follows: >> sd >> An accurate leap-frog stochastic dynamics integrator. Four Gaussian >> random number are required per integration step per degree of freedom. >> With constraints, coordinates needs to be constrained twice per >> integration step. Depending on the computational cost of the force >> calculation, this can take a significant part of the simulation time. >> The temperature for one or more groups of atoms (tc_grps) is set with >> ref_t [K], the inverse friction constant for each group is set with >> tau_t [ps]. The parameter tcoupl is ignored. The random generator is >> initialized with ld_seed. When used as a thermostat, an appropriate >> value for tau_t is 2 ps, since this results in a friction that is >> lower than the internal friction of water, while it is high enough to >> remove excess heat (unless cut-off or reaction-field electrostatics is >> used). NOTE: temperature deviations decay twice as fast as with a >> Berendsen thermostat with the same tau_t. >> >> It is not clear what is the purpose of this integrator and how is it >> different from ld. Can someone refer me to a paper? > > See manual section 3.8 and ref therein. > >> Can such an integrator help in making trajectories less deterministic? > > It's still going to be deterministic, because the RNG is. > > Mark > -- > 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 > -- Quaerendo Invenietis-Seek and you shall discover. -- 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
