[gmx-users] pressure and density

[Alexander Alexander]

Dear gromacs user,

I have a system containing a solid surface(18000 atoms) and on top of it a
heptapeptide solvated in water(SOL  9604), after a good minimisation and
NVT equilibration and before production(which will be in NVT ensemble), I
did NPT equilibration (1 bar) for 200 ps and continued to 1 ns as well, the
average pressure results are coming below.
-----------------------
pcoupl                  = Parrinello-Rahman
Pcoupltype          = isotropic             ;;;;semiisotropic
compressibility    = 4.46e-5             ;;;;0.0   4.46e-5
ref_p                      = 1.0                        ;;;1.0    1.0
tau_p                     = 2.0
refcoord-scaling   = com
------------------------

Statistics over 100001 steps [ 0.0000 through 200.0000 ps ], 1 data sets
All statistics are over 1001 points

Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Pressure                   -782.581         39    925.396   -138.729  (bar)


Statistics over 500001 steps [ 0.0000 through 1000.0000 ps ], 1 data sets
All statistics are over 5001 points

Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Pressure                   -746.168         18    921.982    3.41813  (bar)


My first question as always is that if these amount of pressure and their
RMSD together are satisfying the reference pressure of 1 bar that I
considered?

The second question: The water density I got is around 920 kg/m^3 in the
middle of water region and far away from the solid surface, while I was
expecting to get something around 997 kg/m^3 in the region far from the
solid surface. And none of the tools like gmx inset-molecule, gmx solvate
... , does not let me add extra water molecule to the system, then, how I
can increase the density of water in that region?

Thanks in advance for your comments.

Regards,
Alex