[gmx-users] Higher Density than Expected

[Justin Lemkul]

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

==================================================