Hello, The set pressure should reflect whatever system you are trying to model. >
This statement is not very clear to me.. But when the mdout.mdp file after grompp during energy minimization is examined it says - gen-vel = no gen-temp = 300 gen-seed = 173529 Even though I have not assigned any velocities in em.mdp file. Thats the reason why got this doubt about temperature during energy minimization. Thank you With Regards Kavya > > -Justin > > Thank you >> With Regards >> Kavya >> >> On Mon, Oct 17, 2011 at 3:29 PM, bipin singh <bipinel...@gmail.com<mailto: >> bipinel...@gmail.com>> 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 <hmkv...@gmail.com >> <mailto:hmkv...@gmail.com>> 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 gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> >> > >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> > Please search the archive at >> > >> http://www.gromacs.org/**Support/Mailing_Lists/Search<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 >> <mailto:gmx-users-request@**gromacs.org<gmx-users-requ...@gromacs.org> >> >. >> >> > Can't post? Read >> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > >> >> >> >> -- >> ----------------------- >> Regards, >> Bipin Singh >> -- >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> >> >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> Please search the archive at >> >> http://www.gromacs.org/**Support/Mailing_Lists/Search<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 >> <mailto:gmx-users-request@**gromacs.org<gmx-users-requ...@gromacs.org> >> >. >> >> Can't post? Read >> http://www.gromacs.org/**Support/Mailing_Lists<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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >
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