1. Pressure For my initial configuration, I run a long nvt run. This gives me a pressure. Then I run an npt simulation at this prerssure.
The idea is to do expansion runs(decrease pressure so that the system expands) to get a P vs density curve. For example, after I determine the pressure of the initial configuration from the long nvt run, say Pinit, I choose a set of pressures - Pinit, P1, P2...., PN s.t Pinit>P1,>P2...(eg. 74, 72, 70, 69.....50). Then for each pressure I run an npt simulation till the average converges. 2. Freeze-dimension Is there a better alternative for running simulations for a planar system? Pooja On Thu, Jul 15, 2010 at 10:02 AM, Justin A. Lemkul <[email protected]> wrote: > > > Sai Pooja wrote: > > <snip> > > > Do you run any equilibration prior to applying these parameters? >> Both N-H and P-R allow for wide fluctuations in temperature and >> pressure, respectively, which are exacerbated by systems that are >> not sufficiently equilibrated. Hence it could take a very long time >> if you do not equilibrate well using, i.e. a weak coupling scheme >> first. >> >> >> I usually start with a pressure nearby. For example, I start with a system >> which was equilibrated at p=71 and then run npt at p=69. Is that not >> sufficient? >> >> > How do you determine the pressure before the simulation has begun? > Moreover, freezing your system in one dimension can certainly complicate > matters, since that is a non-equilibrium restraint on the dynamics. That > could be a factor. > > -Justin > > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Quaerendo Invenietis-Seek and you shall discover.
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