Hello, Yes, I have come across that but If the temperature is below the boiling point its fine. But if it crosses the boiling temperature in order keep the water as liquid isnt it necessary to increase the pressure. I understand that the water models do not exactly predict the transition temperature. So in what way does this behaviour of water effect the simulation of a protein?
Thank you With Regards kavya On Mon, Oct 17, 2011 at 5:13 PM, bipin singh <[email protected]> wrote: > 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 >
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