Its basically a melting process and there is ample of published data on this (not related to gromacs though). The only reason for using freeze-dimensions was to avoid using pbc=xy in combination with walls since I thought the extra interactions due to the walls might make the simulations computationally intensive.
The data I have obtained from these runs doesn't seem to match with an npt MC simulation(fortran based in-house code) and the data from the MC simulation looks more credible when compared to published results. Pooja On Thu, Jul 15, 2010 at 10:21 AM, Justin A. Lemkul <[email protected]> wrote: > > > Sai Pooja wrote: > >> >> 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? >> >> > Maybe you want to use "pbc = xy" or walls? Is there any literature > precedent for what you want to do, or perhaps an alternate procedure? > > -Justin > > >> Pooja >> >> >> On Thu, Jul 15, 2010 at 10:02 AM, Justin A. Lemkul <[email protected]<mailto: >> [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 <http://vt.edu> | (540) 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list [email protected] >> <mailto:[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] >> <mailto:[email protected]>. >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> >> -- >> Quaerendo Invenietis-Seek and you shall discover. >> > > -- > ======================================== > > 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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