[gmx-users] Higher Density than Expected

[Christopher Schlicksup]

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
>