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On 08/22/2010 05:29 PM, poj...@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: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAkxxRgEACgkQLpNNBb9GiPnrTwCfSdhm332DXZpgAe7cyVW+q/X9 BIUAoLVw0Ve73jW6aMbPu3w4RpVkjU53 =BUr8 -----END PGP SIGNATURE----- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
