[gmx-users] Metallic boundary conditions

[pojeda at icp.uni-stuttgart.de]

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.