[gmx-users] High Pressure with Martini system

[Tsjerk Wassenaar]

Hi Ricardo,

I think 0.47 should be fine. For normal W you can also increase -solr to
get a bit less ordering, although you need to be careful with large
systems. It should also be possible to add a certain number of antifreeze
particles, but I think you should be fine converting to PW after a short
equilibration with W.

Cheers,

Tsjerk
On Apr 25, 2014 8:54 PM, "Ricardo O. S. Soares" <rsoares at fcfrp.usp.br>
wrote:

> 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
> > >
> > > --
> > > 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-request at 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? 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-request at 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? 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-request at gromacs.org.
>