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

[Mark Abraham]

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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