[gmx-users] Metallic boundary conditions
pojeda at icp.uni-stuttgart.de
pojeda at icp.uni-stuttgart.de
Sun Aug 22 17:29:23 CEST 2010
Hi,
I want to use metallic boundary conditions in my problem.
I think one can do that with the option epsilon_r =0 in gromacs.
If I set epsilon_r =0 I get the output:
Starting 2 threads
Making 1D domain decomposition 2 x 1 x 1
starting mdrun 'Dipoles'
10000000 steps, 5000.0 ps.
Segmentation fault
With other values of epsilon (epsilon=1) the script works well.
and the .log file says:
Constraining the coordinates at t0-dt (step 0)
RMS relative constraint deviation after constraining: 3.33e-07
Initial temperature: 300.135 K
Started mdrun on node 0 Sun Aug 22 17:23:15 2010
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
9.37218e+04 -5.17070e+02 0.00000e+00 nan nan
Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
nan nan nan nan -5.57291e+02
Pressure (bar) Constr. rmsd
nan nan
My question is how could I introduce the metallic boundary
conditions? The input file reads:
; RUN CONTROL PARAMETERS
integrator = md
; Start time and timestep in ps
tinit = 0
;dt = 0.00278089542
dt = 0.0005
nsteps = 10000000
; For exact run continuation or redoing part of a run
init_step = 0
; mode for center of mass motion removal
comm-mode = Linear
; number of steps for center of mass motion removal
nstcomm = 1000
; group(s) for center of mass motion removal
comm-grps =
; OUTPUT CONTROL OPTIONS
; Checkpointing helps you continue after crashes
nstcheckpoint = 5000000
; Output frequency for energies to log file and energy file
nstlog = 1000
nstenergy = 1000
; Output frequency and precision for xtc file
nstxout =1000
nstvout =1000
nstfout =1000
nstxtcout = 1000
xtc-precision = 10
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps =
; Selection of energy groups
energygrps =
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 10
; ns algorithm (simple or grid)
ns_type = grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc = xyz
; nblist cut-off
rlist = 0.9
;SOLVENT
implicit_solvent = no
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = pme
rcoulomb-switch = 0
rcoulomb = 0.9
; Dielectric constant (DC) for cut-off or DC of reaction field
epsilon-r = 0
;epsilon-rf = 0
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths
rvdw-switch = 0
rvdw = 0.9
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension = 1
; Spacing for the PME/PPPM FFT grid
;fourierspacing = 0.07
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx = 32
fourier_ny = 32
fourier_nz = 32
; EWALD/PME/PPPM parameters
pme_order = 6
ewald_rtol = 1e-05
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = yes
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl = nose-hoover
; Groups to couple separately
tc-grps = System
; Time constant (ps) and reference temperature (K)
tau_t = 0.1
ref_t = 300.788
; Pressure coupling
;Pcoupl = berendsen
;Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
;tau_p = 0.1
;compressibility = 4.5e-5
;ref_p = 20000.0
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = yes
gen_temp = 300.788
gen_seed = -1
; OPTIONS FOR BONDS
constraints = all-bonds
; Type of constraint algorithm
constraint-algorithm = Lincs
; Do not constrain the start configuration
unconstrained-start = no
; Use successive overrelaxation to reduce the number of shake iterations
Shake-SOR = no
; Relative tolerance of shake
shake-tol = 1e-04
; Highest order in the expansion of the constraint coupling matrix
lincs-order = 4
; Number of iterations in the final step of LINCS. 1 is fine for
; normal simulations, but use 2 to conserve energy in NVE runs.
; For energy minimization with constraints it should be 4 to 8.
lincs-iter = 1
; Lincs will write a warning to the stderr if in one step a bond
; rotates over more degrees than
lincs-warnangle = 20
; Convert harmonic bonds to morse potentials
morse = no
thank you in advance.
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