[gmx-users] Density Differences

[Kavyashree M]

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.
>
> 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>> 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 at gromacs.org
>>    <mailto:gmx-users at 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-request at gromacs.org
>>    <mailto:gmx-users-request at 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 at 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110413/4faf5bb7/attachment.html>