On Sun, May 16, 2010 at 7:41 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > Amit Choubey wrote: > >> >> >> On Sun, May 16, 2010 at 5:15 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> Amit Choubey wrote: >> >> Hi Justin, >> >> Since the density (1 gm/cc) and T (300 K) correspond to ambient >> condition, should not the equation of state dictate a pressure >> around 1 atm? >> >> >> If the equation of state involves temperature and pressure, yes. >> >> So if you fix the density and temperature shouldnt you land up with right >> pressure which we know should be 1 atm. >> >> > > You are not fixing (or conserving) the temperature in an NVE ensemble. > That would be an NVT ensemble, employing a thermostat. I did do NVT first and then for sampling i removed the thermostat. Also as you mentioned there was not much difference b/n pressure values during NVT or NVE . The pressure value is as high as 1000 bar in both cases. > Since instantaneous pressure is calculated (in part) from the kinetic > energy, and since the kinetic energy is not guaranteed to be conserved, the > pressure term will also fluctuate accordingly. > This is correct. The pressure thus fluctuates about 20 % of the above mentioned value. > > http://www.gromacs.org/Documentation/Terminology/Pressure > > The internal energy of the system is constant in an NVE ensemble, the other > terms may fluctuate as necessary such that all microstates occur with the > same probability and the energy surface remains flat. I agree > Also recall that an NVE ensemble represents a thermodynamically isolated > system, not conducting heat or engaging in work with the surrounding system. > true > So any concept of external pressure and equilibrating the pressure is > irrelevant. > I am not trying to equilibriate the pressure. I am trying to measure the pressure. I also know that at 300 K and 1gm/cc the P should be 1 bar. Also, theoretically NVE or NVT are no different than NPT as far as measuring observables is concerned. Hence i was thinking that if you have the right volume density and temperature shouldnt you have the right pressure. > > -Justin > > amit >> >> >> >> thank you >> amit >> >> >> On Sun, May 16, 2010 at 2:07 PM, Justin A. Lemkul >> <jalem...@vt.edu <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote: >> >> >> >> Amit Choubey wrote: >> >> Hi Everyone, >> >> I was doing MD with SPC waters and found something which i >> am >> not sure how to explain. >> >> I made a box of SPC water of dimension 4x4x4 nm^3 and filled >> with water using grenbox . >> >> I then did a nvt simulation at 300 K for 1 ns . I used >> berendsen >> coupling and Reaction - Field for coulomb interaction. >> Cut off >> were all set to 1 nm. Temperature did converge to 300 K. >> After >> this i turned of nvt and did nve with RF-zero for another >> ns. >> Energy was well converged during this (RMSD < 0.1 %). >> Temperature was also around 304 K (RMSD < 1%). But the >> pressure >> was 1.1 Kilobar with a fluctuation of 20 % . I don >> understand >> this, shouldnt this be around 1 bar ? Could some one suggest >> whats on ? >> >> >> Since an NVE ensemble employs neither a thermostat nor a >> barostat, I >> don't know why you'd expect that. >> >> -Justin >> >> Thank you, >> amit >> >> >> -- ======================================== >> >> 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> <http://vt.edu> | (540) >> >> 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>> >> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/searchbefore >> 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-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>. >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> -- ======================================== >> >> 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 gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> 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 gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> > -- > ======================================== > > 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 gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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