[gmx-users] Density Differences
Justin A. Lemkul
jalemkul at vt.edu
Wed Apr 13 14:52:52 CEST 2011
Kavyashree M wrote:
> 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?
>
That's a 2.6% difference. I wouldn't call that "nowhere close." Unless you are
literally reproducing the exact same system used during parameterization (which
you're not, based on your system contents and the use of algorithms like PME
that didn't exist in 1983) then you shouldn't necessarily expect identical results.
-Justin
>
> On Wed, Apr 13, 2011 at 6:03 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at 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
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at 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> <http://vt.edu> | (540)
> 231-9080
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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> --
> ========================================
>
> 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
>
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--
========================================
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
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