[gmx-users] Density Differences

[Kavyashree M]

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.

Thanking you
With regards
Kavya

On Wed, Apr 13, 2011 at 5:38 PM, Justin A. Lemkul <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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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