On Sun, Jun 26, 2016 at 12:04 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: Hello Mark and thank you for your response.
> Hi, > > On Sat, Jun 25, 2016 at 5:27 PM Alexander Alexander < > alexanderwie...@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 > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? 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