Re: [gmx-users] How to prevent box shrinking incessantly at x and y when doing membrane simulation using semiisotropic couple type?
Dear Chris Thanks again for your reply. On Sat, Jun 2, 2012 at 10:52 PM, Christopher Neale chris.ne...@mail.utoronto.ca wrote: I suspect that you can find an equation to relate the surface tension to the ratio of the pressure along z to the pressure along xy that is required to maintain the unit cell of a semi-isotropic simulation approximately constant when you use the same compressibility in all dimensions. Actually there is an equation to calculate surface tension by lateral pressure and normal pressure. [image: Inline image 1] 1/2 shows there are two interfaces. Lz is the lenth of box-z. Pn(Z) is normal pressure. Pt(Z) is (press-x + press-y)/2. But pressure must be gotten by correct simulation. You might even find an equation that was based on the rate of unit cell deformation when applying the same pressure in all dimensions. Since this is a non-equilibrium simulation you may need to run many of them to get an average rate. Sorry I don't know how to contact the rate to the surface tension. Or should I use this rate to set my pressure or compressbility? Alternatively, you might consider simulating a spherical glob of decane in a water bath and finding equations that relate the aspherocity to the surface tension. It's interesting and I am thinking about it. It needs a lot of work to do. aha If I were you, I'd look into physics textbooks to find some relation like this that you can use. Chris. -- gmx-users mailing listgmx-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 image.png-- gmx-users mailing listgmx-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
Re: [gmx-users] How to prevent box shrinking incessantly at x and y when doing membrane simulation using semiisotropic couple type?
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.auwrote: 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 listgmx-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?
Re: [gmx-users] How to prevent box shrinking incessantly at x and y when doing membrane simulation using semiisotropic couple type?
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.
