[gmx-users] High Pressure with Martini system

Tsjerk Wassenaar tsjerkw at gmail.com
Sat Apr 26 22:33:52 CEST 2014 

Hi Ricardo,

You can also use insane to build an initial model of the
membrane+protein+solvent, and then solvate that system in a larger box. If
you then run with position restraints on the membrane and the protein, you
should be fine, being able to equilibrate the system, without distorting
the protein/membrane, while avoiding the abnormal pressures.

Cheers,

Tsjerk


On Sat, Apr 26, 2014 at 9:22 PM, Ricardo O. S. Soares
<rsoares at fcfrp.usp.br>wrote:

> Hello Tsjerk,
>
> I found out the the big frozen membrane was causing the extremely large
> pressure, so now I made a box with the same previous dimensions, now filled
> with only W water and ions. The system is running fine.
> After this step, I'm going to convert W to PW and further equilibrate
> it.Then, afterwards I'm thinking about merging this system with the
> membrane and protein, and use g-select to remove the overlap.
> A bit more equilibration and then, hopefully, I'll have a production run.
> Thanks for your suggestions, Tsjerk.
>
> 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 17:59:06
> > Assunto: Re: [gmx-users] High Pressure with Martini system
>
> > 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
> > > > >
> > > > > --
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-- 
Tsjerk A. Wassenaar, Ph.D.

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