[gmx-users] Re: Membrane Runs Crashing

Mirco Wahab mirco.wahab at chemie.tu-freiberg.de
Wed Jun 19 23:16:10 CEST 2013

On 19.06.2013 15:25, Neha wrote:
> Here's the full mdp file. Please let me know if you need anymore information
> and thank you so much for helping!
> dt                       = 0.02

Should be 0.03 according to S. Marrinks own remarks
(but wouldn't change your experience)

> nstcomm                  = 1

This looks much too conservative ;-)

> Pcoupltype               = semiisotropic
> tau_p                    = 1.0  1.0
> compressibility          = 5e-6 0.0
> ref_p                    = 0.0  0.0

This (compressibility = XY  Z) means, the "height" of your
box is not allowed to change? Is this the intended behaviour?

The ref_p of zero should not pose any real problem here,
MARTINI W is a strongly associating fluid and will freeze
trough your box in no time even when setting negative pressure
below 300K. In newer Gromacs versions (from 4.6) there seems
to be additional shift (?) in the potential, so the water phase
transition took another hit and went up to over 320K (with
verlet) and to about 315K (with shift).

I could provide you (*) a large Martini-DPPC-bilayer (~25nm²,
2 x 1330 DPPC), fully solvated in W (98654 W) which is
stable at 0.03ps even with verlet integration, and
semiisotropic Parinello-Rahman coupling at ref_p of { 0, 0},
or {1, 1} or whatever you like. I made this some time ago for
a student's experiment.

It's (at least for me) remarkably complicated to get such a
simple thing like a Martini-bilayer right. You have to
equilibrate the pure-water box (exactly the same box size
as your target system), you have to make sure there are NO
waters later within the bilayer left (after genbox solvation)
  - (I had to write a script to remove the waters at the bilayer
core expicitly).



(*) drop me a e-mail

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