Ok, The protein I am going to simulate is from a hyperthermophilic organism which lives in deep oceanic thermal vents. so in the deep vents the pressure will be enormous. even though I do not have much information about the magnitude of pressure in that site and inside the cell of that organism.. I may be able to get some rough estimate of pressure..
So I wanted to simulate this protein at a temperature near 90 or 100 deg C. Thank you With Regards Kavya On Mon, Oct 17, 2011 at 8:45 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Kavyashree M wrote: > >> Hello, >> >> I am sorry those were two different questions.. I wanted to know what >> this statement actually mean? >> "The set pressure should reflect whatever system you are trying to model." >> >> > You haven't fully explained what exactly you're trying to do yet, so I'm > taking a stab in the dark. Let's say you're trying to simulate a benchtop > experiment with a protein in solution over a heating mantle at 350 K. The > pressure is 1 atm under such circumstances (NPT). Now let's say you want to > simulate the behavior of a protein solution in a bomb calorimeter (constant > volume) at 350 K. The pressure is not likely to be 1 atm under such > circumstances (but then too, you'd use NVT instead of NPT, but maybe after > NPT equilibration at whatever the necessary pressure is). Without a fully > detailed description of what you'd like to accomplish, I'm going to stop > guessing. > > You've asked a lot of scattered questions about different topics, which > makes it less efficient for people to help you and less clear for you to > understand what we're trying to communicate back, even if it is somewhat > generic. > > -Justin > > Thank you >> With Regards >> Kavya >> >> >> I don't see the connection to my comment about pressure, but I'll >> address this anyway. There is no temperature during EM. Hence with >> "gen-vel = no" then no velocities are generated. The settings for >> gen-temp and gen-seed are defaults that are assigned when none are >> provided in the input .mdp file. >> >> I seem to recall that a pressure term is written during EM, but it >> is largely meaningless. >> >> -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<http://vt.edu/Pages/Personal/justin> >> >> <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 >> <mailto:gmx-users@gromacs.org> >> >> http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >> >> >> <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> >> >> >> <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> >> >> <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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