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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