[gmx-users] pressure and density

[Alexander Alexander]

No comment, please?
Regards,
Alex

On Sun, Jun 26, 2016 at 9:52 PM, Alexander Alexander <
alexanderwien2k at gmail.com> wrote:

>
>
> 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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