[gmx-users] Higher Density than Expected

[Christopher Schlicksup]

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

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)