[gmx-users] pressure and density

[Mark Abraham]

Hi,

On Sat, Jun 25, 2016 at 5:27 PM Alexander Alexander <
alexanderwien2k at gmail.com> wrote:

> 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,


That sounds like a proverbial eyeblink. I suggest you take your aqueous
phase and get a feel for how long you have to simulate before you have even
measured the pressure reliably wrt to its fluctuations.


> 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?
>

No. Why is that data more consistent with 1 than 10?

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.


Then you are expecting quite a bit of volume change before you've
equilibrated the density. You should measure the density of your model of
the aqueous phase separately, rather than assume it is standard water.

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?
>

They can add water if you have gaps... but with what density did you
construct your system? Given that, what's the problem with running NPT
until you are happy with the density?

Mark

Thanks in advance for your comments.
>
> Regards,
> Alex
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