[gmx-users] High Pressure with Martini system

[Ricardo O. S. Soares]

Hello Mirco, thanks for your reply. Please check my notes below. 

Ricardo. 

De: "Mirco Wahab" <mirco.wahab at chemie.tu-freiberg.de> 

> Para: "gromacs org gmx-users"
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Enviadas: Sexta-feira, 25 de Abril de 2014 3:03:18
> Assunto: Re: [gmx-users] High Pressure with Martini system

> 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?

The whole system has about 24x10⁶ atoms/beads. Since I used PW (polarizable water, which has 3 'atoms' --> WM, WP, W), I have about 7.5x10^6 molecules, and therefore about 22.5 x 10^6 solvent atoms. 

> 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 ...

I'm just failing to understand why a negative pressure would cause the box to expand, instead of contract... 

> > 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?

The box dimensions are 153.32965 102.32965 62.00000, and I have XXX lipids. 

> What do you expect from the frozen bilayer if you pressure-couple
> your box dimensions?

The bilayer is smaller than the XY dimensions of the box, so I'd expect it to remain frozen until the desired pressure and solvation is reached and then I'd remove the freezing code and probably add some weak restrains in the Z axis, for further equilibration. 

> 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.

That interest me, do you have a reference for this information? thanks. 

> BTW.: what hardware are you on if you expect to equilibrate
> a system of that size (if the 2.4x10^6 figure is correct?)

For this system I'm using a BlueGene/P an SGI Altix XE 1300 . 

> Regards

> M.

> Disclaimer: I did simulate similar MARTINI systems of 1/10th the
> size of yours

I did simulated a smaller (500K atoms) similar system before with no problems, but then again, 24x10^6 isn't 500K ;) 

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