[gmx-users] Density Differences
Kavyashree M
hmkvsri at gmail.com
Wed Apr 13 14:57:11 CEST 2011
Ok Thanks.
On Wed, Apr 13, 2011 at 6:22 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
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