[gmx-users] Density Differences
hmkvsri at gmail.com
Wed Apr 13 14:48:04 CEST 2011
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 <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.
> For the actual target value of TIP4P density, refer to the literature. The
> TIP4P citation is provided in the Gromacs manual.
> Thanking you
>> With regards
>> On Wed, Apr 13, 2011 at 5:38 PM, Justin A. Lemkul <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.
>> Thanking you
>> With regards
>> -- ========================================
>> 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
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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
> gmx-users mailing list gmx-users at gromacs.org
> 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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