[gmx-users] High Pressure with Martini system

[Ricardo O. S. Soares]

Hello Tsjerk, 

You're right, when insanely solvating I sometimes put the water too close or too far. Do you know if 0.47 is a good value for the -sold parameter? 
>From my experience with Martini-W beads and a small bilayer, I usually find that the system tends to freeze. 
However, I think that this happens after the pressure reaches a reasonable value, so I could in this moment use the triple-w.py script to replace W for PW, right? 
And then, like you said, perform NVT and NpT equilibration. .. 

Thanks for your input, 

Best, 

Ricardo. 

--- 
Biological Chemistry and Physics 
Faculty of Pharmaceutical Sciences at Ribeirão Preto 
University of São Paulo - Brazil 
----- Mensagem original -----

> De: "Tsjerk Wassenaar" <tsjerkw at gmail.com>
> Para: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Enviadas: Sexta-feira, 25 de Abril de 2014 3:31:52
> Assunto: Re: [gmx-users] High Pressure with Martini system

> Hi Ricardo,

> Insanely built systems with polarizable watets may be tricky,
> especially if
> the system is large (not to say humongous). Maybe it's worth adding a
> stage
> using normal Martini water, let that equilibrate (NVT and NpT), and
> then
> add in the polarizable sites, letting the system equilibrate again
> (NVT,
> since the system size should pretty much match the equilibrium
> pressure
> density).

> Cheers,

> Tsjerk
> On Apr 25, 2014 8:06 AM, "Mirco Wahab"
> <mirco.wahab at chemie.tu-freiberg.de>
> wrote:

> > On 25.04.2014 00:07, Ricardo O. S. Soares wrote:
> >
> >> I ran an NVT equilibration of a 24mi CG Martini atoms and detected
> >> the
> >> formation of vacuum spots on the solvent.
> >>
> >
> > CG Martini has many sphere types, did you solvate your system
> > with 24x10^6 MARTINI-W segments?
> >
> > MARTINI-W is is strongly association LJ-fluid. In large,
> > inhomogeneous
> > systems (non-optimal box solvation) it is expected to generate huge
> > forces if either too-close or not close enough packed.
> >
> > However, the log file shows a very large negative pressure (about
> > -4e+28)
> >> all the time, since the beginning.
> >> Despite the negative pressure, when I turn pressure coupling ON,
> >> the very
> >> first step causes the box to expand (!) too much and then the
> >> simulation
> >> crashes.
> >>
> >
> > there you are ...
> >
> > Things I tried, and failed: changed the tau_p to several values (1
> > to
> >> 500); changed the compressibility; changed the ref_p from 1 to
> >> values
> >> closer to the starting pressure; changed time-step from 0.02 up to
> >> 0.0005.
> >> Additional info: used the insane.py script to solvate the box with
> >> polarizable water; there's a large (frozen) bilayer at the center
> >> of the
> >> box, It, however is smaller than the box sides, to it doesn't
> >> interact with
> >> itself via PBC.
> >> I'm sure I could provide more info, so please ask me for the
> >> specifics
> >> and I'll reply.
> >>
> >
> > How large is the box, is it cubic? How many Lipids in the bilayer?
> > What do you expect from the frozen bilayer if you pressure-couple
> > your box dimensions?
> >
> > Be warned that the MARTINI-Lipids constitute bilayers which are
> > very "floppy" and spontaneously fold into spheres (vesicles) if
> > the aggregate has more than around 600 Molecules.
> >
> > BTW.: what hardware are you on if you expect to equilibrate
> > a system of that size (if the 2.4x10^6 figure is correct?)
> >
> > Regards
> >
> > M.
> >
> > Disclaimer: I did simulate similar MARTINI systems of 1/10th the
> > size of yours
> >
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