Well,as I found in literatures people have used same( 1 atm) pressure at high temperature simulations(NPT simulations). with different water models.As most of the force field parameters are determined generally at 300K and 1 atm. What would be the the possible drawbacks of using the same pressure(or even high pressure) at different temperatures(300K-400K ranges) for a given force field.
On Mon, Oct 17, 2011 at 17:04, Justin A. Lemkul <[email protected]> wrote: > > > Kavyashree M wrote: >> >> Thank you, >> >> What about the pressure that need to be used at that temperature >> (for a system of a protein in tip4p water) >> > > The set pressure should reflect whatever system you are trying to model. > > -Justin > >> Thank you >> With Regards >> Kavya >> >> On Mon, Oct 17, 2011 at 3:29 PM, bipin singh <[email protected] >> <mailto:[email protected]>> wrote: >> >> As far as I know we do energy minimization at room temperature only. >> Only during equilibration >> (NVT and NPT) we use high temperature for maintaining proper density >> before starting the final production run. >> >> On Mon, Oct 17, 2011 at 15:15, Kavyashree M <[email protected] >> <mailto:[email protected]>> wrote: >> > Dear users, >> > >> > For simulating a protein at high temperature (more than 300K, >> > less than 400K) using OPLSAA forcefield, what are the parameters >> > other than Temperature that need to be taken care of? >> > Does the energy minimization step also needs to be done at high >> > temperature? (here my aim is not to simulate an unfolding event) >> > I have a reference - >> > Biophysical Journal Volume 94 June 2008 4444–4453 >> > >> > Any other references or suggestions will be helpful. >> > >> > Thanking you >> > With Regards >> > M. Kavyashree >> > >> > >> > -- >> > 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/Support/Mailing_Lists/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/Support/Mailing_Lists >> > >> >> >> >> -- >> ----------------------- >> Regards, >> Bipin Singh >> -- >> 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/Support/Mailing_Lists/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/Support/Mailing_Lists >> >> > > -- > ======================================== > > 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/Support/Mailing_Lists/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/Support/Mailing_Lists > -- ----------------------- Regards, Bipin Singh -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
