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

[Klniu]

Sorry for my carelessness. Before nose-hoover, Parrinello-Rahman, I have
done v-rescale, berendsen already. tau_t = 0.1, tau_p = 0.5.

Hugh.

On Sat, Jun 2, 2012 at 12:43 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  On 2/06/2012 1:11 PM, Klniu wrote:
>
> 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?
>
>
> Equilibration with P-R pressure coupling is asking for trouble. Use
> Berendsen to get close, then switch. Otherwise, see
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up
>
> Mark
>
>
>
>  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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