The original paper (J. Chern. Phys., Vol. 79, No.2, 15 July 1983) stated a density of 0.999g/cc at 298K and 1atm, which is nowhere close to the value i have got. (1.025g/cc). or is this value tolerable?
On Wed, Apr 13, 2011 at 6:03 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Kavyashree M wrote: > >> I am sorry I did not include it in the mail: i used the following: >> >> pcoupl = Parrinello_Rahman pcoupltype = >> isotropic tau_p = 2.0 >> compressibility = 4.5e-5 ref_p = 1.0 >> >> I agree that density of water is different depending on the model used, >> so for tip4p water what is the range of fluctuations accepted? So that >> we can conclude that the difference is not due to any other reason but >> the water model used. >> >> > The extent of fluctuation in any pressure-related term depends on the size > of your system and several of the .mdp settings. > > http://www.gromacs.org/Documentation/Terminology/Pressure > > For the actual target value of TIP4P density, refer to the literature. The > TIP4P citation is provided in the Gromacs manual. > > -Justin > > Thanking you >> With regards >> Kavya >> >> On Wed, Apr 13, 2011 at 5:38 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> Kavyashree M wrote: >> >> Dear gromacs users, >> I am trying to simulate a 225aa protein at 300K in water, >> with OPLSAA force filed, tip4p water model, using the >> parameters below (for pressure equilibration) during >> >> >> You're not doing NPT. You haven't specified pcoupl or any of the >> other relevant parameters, so you're doing NVT. >> >> >> position restrained md. >> >> integrator = md dt >> = 0.002 nsteps = 50000 >> nstcomm = 10 nstlist >> = 5 ns_type = grid pbc >> = xyz rlist = 1.40 >> coulombtype = PME rcoulomb = 1.40 >> vdwtype = Switch rvdw_switch >> = 0.9 rvdw = 1.00 >> fourierspacing = 0.12 pme_order >> = 4 ewald_rtol = 1e-5 >> optimize_fft = yes Tcoupl = nose-hoover >> tc_grps = Protein Non-Protein >> tau_t = 0.4 0.4 ref_t >> = 300 300 nh-chain-length = 1 >> gen_vel = no continuation = yes >> constraints = all-bonds >> constraint-algorithm = LINCS >> lincs-order = 4 lincs-iter = >> 1 lincs-warnangle = 30 >> when I calculate the densities, the average came out to be >> 1025.91 kg/m^3, >> Could anyone please clarify me the reason for this density. >> >> >> Simulating with the right ensemble (NPT) will equilibrate the >> pressure and thus density. As a fundamental point, please also >> realize that each water model has its own (different) expected >> density value, which is also influenced somewhat by the remaining >> contents of the system. Therefore, the result you obtain may not be >> in exact agreement with experimental bulk density of water. >> >> -Justin >> >> >> Thanking you >> With regards >> Kavya >> >> >> -- ======================================== >> >> 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/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-requ...@gromacs.org>. >> >> 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 gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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