[gmx-users] pressure and density

[Alexander Alexander]

On Sun, Jun 26, 2016 at 12:04 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:
Hello Mark and thank you for your response.

> 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.
>

Actually I had simulated the aqueous phase of my system containing water
and heptapeptide which could reach to equilibration of both pressure and
density easily in 200 ps of NPT.


>
>
> > 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?
>

Of course I am looking for 1 bar not 10. Any way I repeated the NPT
equilibration by the "berendsen" pressure coupling and the the average
pressure come really close to 1 bar as you can see below:

Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Pressure                    1.99668       0.82     108.19   -3.28499  (bar)


> 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.
>

Here are the unit cell or box size initially and after NPT isotropic
equilibration for 200, 1000 and 1500 ps respectively.
Initiall:
X                   Y             Z(nm)
6.59210   7.78590   9.23350

200 ps:
6.59505   7.78938   9.23763

1000 ps
6.59450   7.78874   9.23686

1500 ps:
6.59464   7.78890   9.23706

the the system size should not change too much as these number in x-y
direction are originated from unit cell of a solid crystal structure.
With all these I think the system has been equilibrated to a reasonable
pressure closed to reference of 1 bar but I am still worry about water
density which is around 920 kg/m^3 so far.
I also tried the semiisotropic to have change only in the Z direction, but
the result is disaster.

Thanks.
Alex


>
> 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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