[gmx-users] Metallic boundary conditions

[Florian Dommert]

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On 08/22/2010 05:29 PM, pojeda at icp.uni-stuttgart.de wrote:
> 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:
> 

Metallic boundries are set with epsilon_surface=0

/Flo

> 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.
> 
> 
> 
> 
> 
> 
> 


- -- 
Florian Dommert
Dipl.-Phys.

Institute for Computational Physics

University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

Phone: +49(0)711/685-6-3613
Fax:   +49-(0)711/685-6-3658

EMail: dommert at icp.uni-stuttgart.de
Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
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