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.abra...@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. > > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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