[gmx-users] How to prevent box shrinking incessantly at x and y when doing membrane simulation using semiisotropic couple type?

[Klniu]

Dear Gromacs users,

I am doing a membrane simulation. The system are two layers composed
by surfactants. other molecule are decane and water. The system like
this:

decane

---------------

surfactant
> ---------------

water
> ---------------

surfactant

---------------

decane

My research is to get the surface tension  between decane and water. I
mainly use NPT simulation to reach equilibrium and product.

when I set pcoupl = semiisotropic and compressibility  = 4.5e-5 4.5e-5, the
box at x and y will shrink incessantly and then the system crashes.

My question is:
1. Is my direction of work worng? There is another way to do this simution?
2. how can I get surface tension?

The content of mdp file is below:

> ; NEIGHBORSEARCHING PARAMETERS
>
> ; nblist update frequency
>
> nstlist                  = 10
>
> ; ns algorithm (simple or grid)
>
> ns_type                  = grid
>
> ; Periodic boundary conditions: xyz, no, xy
>
> pbc                      = xyz
>
> periodic_molecules       = no
>
> ; nblist cut-off
>
> rlist                    = 1.0
>
> ; long-range cut-off for switched potentials
>
> rlistlong                = -1
>
>
>> ; OPTIONS FOR ELECTROSTATICS AND VDW
>
> ; Method for doing electrostatics
>
> coulombtype              = PME
>
> rcoulomb-switch          = 0
>
> rcoulomb                 = 1.0
>
> ; Relative dielectric constant for the medium and the reaction field
>
> epsilon_r                = 1
>
> epsilon_rf               = 1
>
> ; Method for doing Van der Waals
>
> vdw-type                 = Cut-off
>
> ; cut-off lengths
>
> rvdw-switch              = 0
>
> rvdw                     = 1.4
>
> ; Apply long range dispersion corrections for Energy and Pressure
>
> dispcorr                 = EnerPres
>
> ; Extension of the potential lookup tables beyond the cut-off
>
> table-extension          = 1
>
> ; Seperate tables between energy group pairs
>
> energygrp_table          =
>
> ; Spacing for the PME/PPPM FFT grid
>
> fourierspacing           = 0.135
>
> ; FFT grid size, when a value is 0 fourierspacing will be used
>
> fourier_nx               = 0
>
> fourier_ny               = 0
>
> fourier_nz               = 0
>
> ; EWALD/PME/PPPM parameters
>
> pme_order                = 4
>
> ewald_rtol               = 1e-05
>
> ewald_geometry           = 3d
>
> epsilon_surface          = 0
>
> optimize_fft             = yes
>
>
>> ; IMPLICIT SOLVENT ALGORITHM
>
> implicit_solvent         = No
>
>
>> ; GENERALIZED BORN ELECTROSTATICS
>
> ; Algorithm for calculating Born radii
>
> gb_algorithm             = Still
>
> ; Frequency of calculating the Born radii inside rlist
>
> nstgbradii               = 1
>
> ; Cutoff for Born radii calculation; the contribution from atoms
>
> ; between rlist and rgbradii is updated every nstlist steps
>
> rgbradii                 = 1
>
> ; Dielectric coefficient of the implicit solvent
>
> gb_epsilon_solvent       = 80
>
> ; Salt concentration in M for Generalized Born models
>
> gb_saltconc              = 0
>
> ; Scaling factors used in the OBC GB model. Default values are OBC(II)
>
> gb_obc_alpha             = 1
>
> gb_obc_beta              = 0.8
>
> gb_obc_gamma             = 4.85
>
> gb_dielectric_offset     = 0.009
>
> sa_algorithm             = Ace-approximation
>
> ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
>
> ; The value -1 will set default value for Still/HCT/OBC GB-models.
>
> sa_surface_tension       = -1
>
>
>> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
>
> ; Temperature coupling
>
> tcoupl                   = Nose-Hoover
>
> nsttcouple               = -1
>
> nh-chain-length          = 10
>
> ; Groups to couple separately
>
> tc-grps                  = OIL DRG SOL
>
> ; Time constant (ps) and reference temperature (K)
>
> tau_t                    = 0.5 0.5 0.5
>
> ref_t                    = 300 300 300
>
> ; Pressure coupling
>
> pcoupl                   = Parrinello-Rahman
>
> pcoupltype               = semiisotropic
>
> nstpcouple               = -1
>
> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
>
> tau_p                    = 2.0 2.0
>
> compressibility          = 4.5e-5 4.5e-5
>
> ref_p                    = 1.0 1.0
>
>
I have post a mail in list but my description is not clear.
http://lists.gromacs.org/pipermail/gmx-users/2012-June/072000.html

Thank you.

Hugh.
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