[gmx-users] Higher Density than Expected

[Tsjerk Wassenaar]

Hey :)

Salt water has a higher density than pure water anyway.

Cheers,

Tsjerk
On Apr 26, 2016 5:19 PM, "Christopher Schlicksup" <cschlick at umail.iu.edu>
wrote:

> Thanks Justin. I was expecting closer to 1000kg/m^3. My reading about the
> tip3p water model found approximately this value at 300K, and it is also
> the approximate experimental value. So I guess my question was whether
> 1025kg/m^3 was off enough to be a concern.
>
> I think you answered the question: that the system is too inhomogeneous to
> pay that close attention to the absolute density value. Thanks again.
>
>
>
> > Date: Mon, 25 Apr 2016 17:13:01 -0400
> > From: Justin Lemkul <jalemkul at vt.edu>
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Higher Density than Expected
> > Message-ID: <571E885D.2030001 at vt.edu>
> > Content-Type: text/plain; charset=windows-1252; format=flowed
> >
> >
> >
> > On 4/25/16 5:09 PM, Christopher Schlicksup wrote:
> > > Hi, I am fairly new to simulation, and would like some input about
> > whether
> > > I have set up Gromacs correcly. I am using version 5.0.4 with the
> > > CHARMM36-Jun2015 force field and the TIP3P water model. I am
> simulating a
> > > 35kDa protein in a dodecahedron box (-d 1.6) with 150mM NaCl plus
> > > neutralizing ions.
> > >
> > > I do a 200ps NVT equilibration followed by a 500ps NPT equilibration
> > > followed by 230ps of production run where the protein is unrestrained.
> My
> > > observations so far are that the density is higher than I would expect
> > from
> > > reading literature. I would appreciate any insight into whether I have
> a
> > > problem, or if my density and pressure values look acceptable. Thanks
> in
> > > advance
> > >
> >
> > What value do you expect from the literature?  The density of such an
> > inhomogeneous system is rather useless.  Everything looks fine to me.
> >
> > -Justin
> >
> > > Here are my results from gmx energy:
> > >
> > > *Energy minimization*
> > >
> > > Energy                      Average   Err.Est.       RMSD  Tot-Drift
> > >
> >
> -------------------------------------------------------------------------------
> > > Potential                -1.93229e+06      29000    77735.5    -189748
> > > (kJ/mol)
> > >
> > >
> > > *NVT Equilibration 200ps*
> > >
> > > Energy                      Average   Err.Est.       RMSD  Tot-Drift
> > >
> >
> -------------------------------------------------------------------------------
> > > Temperature                   299.9      0.099    2.59846   0.560458
> (K)
> > >
> > >
> > > *NPT Equilibration 500ps*
> > >
> > > Energy                      Average   Err.Est.       RMSD  Tot-Drift
> > >
> >
> -------------------------------------------------------------------------------
> > > Pressure                    1.52892        1.7    81.0079    11.2974
> > (bar)
> > > Density                     1024.74      0.057    1.70907 -0.0499058
> > > (kg/m^3)
> > > Volume                      1168.76      0.065    1.96293  0.0505822
> > (nm^3)
> > >
> > >
> > > *Production Run 230ps*
> > >
> > > Energy                      Average   Err.Est.       RMSD  Tot-Drift
> > >
> >
> -------------------------------------------------------------------------------
> > > Pressure                   0.450022       0.65    75.3012   0.157248
> > (bar)
> > > Density                      1025.4      0.048    1.39937  -0.209504
> > > (kg/m^3)
> > > Volume                      1168.01      0.055    1.59374   0.238338
> > (nm^3)
> > >
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> --
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