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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