[gmx-users] High Pressure with Martini system

[Tsjerk Wassenaar]

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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