Hi, I don't see any immediate problem in your file, except the fact that you have to couple all molecule to a heat bath. Second, has much as I know, you can't reach 0K, so what the meaning?
Best, Itamar On Tue, Jun 2, 2009 at 9:11 PM, Inon Sharony <[email protected]> wrote: > Hi everyone! > > I'm trying to run a simulation of a single diatomic Sulfur molecule. When I > run an equilibration scheme (generating velocities from a 300K > Maxwell-Boltzmann distribution) it runs fine, but when I take the > equilibrated molecule and couple one atom to a 0K heat bath (using > Stochastic Dynamics) the simulation segfaults at the first step. > > I've enclosed as much information as I could. Notice (at the very bottom) > that the md.log file shows an initial temperature of 17884.7K, but already > in the report for step 0 the temperature, as well as many other > thermodynamic quantities, are NaN. > > I've encountered one reference to the same error I'm getting, but itjust > said that there was some problem with the input files, but didn'tsay what > was the problem... > > I hope you will find some stupid mistake in the *.mdp file, or something > easily remedied... > > P.S. > > I know GROMACS is not optimized for simulating tiny molecules, but I don't > see why it should be such a critical problem... > > > A wholotta supplemental data: > > > MDRUN_MPI STD-I/O: > ================== > > step 0 > [hydrogen:15285] *** Process received signal *** > [hydrogen:15285] Signal: Segmentation fault (11) > [hydrogen:15285] Signal code: Address not mapped (1) > [hydrogen:15285] Failing at address: 0xfffffffe16c50a90 > [hydrogen:15285] [ 0] /lib64/libpthread.so.0 [0x355c00de80] > [hydrogen:15285] [ 1] mdrun_mpi(gmx_pme_do+0x28b2) [0x4b56f2] > [hydrogen:15285] [ 2] mdrun_mpi(do_force_lowlevel+0x1023) [0x47f6f3] > [hydrogen:15285] [ 3] mdrun_mpi(do_force+0xe6e) [0x4c99ce] > [hydrogen:15285] [ 4] mdrun_mpi(do_md+0x48f0) [0x42c4a0] > [hydrogen:15285] [ 5] mdrun_mpi(mdrunner+0x831) [0x42d771] > [hydrogen:15285] [ 6] mdrun_mpi(main+0x3c0) [0x42e6a0] > [hydrogen:15285] [ 7] /lib64/libc.so.6(__libc_start_main+0xf4) > [0x355b41d8b4] > [hydrogen:15285] [ 8] mdrun_mpi [0x4131a9] > [hydrogen:15285] *** End of error message *** > ./test-2-6-09.sh: line 16: 15285 Segmentation fault mdrun_mpi -c md -v > > > > ---------------------------------------------------------------------------------------------------------------- > > MD.MDP > ====== > > integrator = sd ;stochastic dynamics (velocity Langevin) using a > leap-frog algorithm > dt = 0.0001 > nsteps = 10000 ; [steps] ==> total > (nsteps*dt) ps. > nstxout = 1 > nstvout = 1 > nstfout = 1 > ; nstxtcout = 1 > nstenergy = 1 ; write energies to energy file every 1000 steps > (default 100) > nstlog = 1 > energygrps = SL SR > ns_type = simple > periodic_molecules = no > coulombtype = PME > tc-grps = SL SR > tau_t = 0 1 ; mass/gamma > ref_t = 0 0 ; refference (bath) temperature > Pcoupl = no > gen_vel = no > gen_seed = -1 ; random seed based on computer clock > constraints = none > > > -------------------------------------------------------------------------------------------- > > 1S2.itp > ======= > > [ atomtypes ] > ;atomtype m (u) q (e) part.type V(cr) W(cr) > SX 32.0600 0.000 A 1E-03 1E-05 > > [ moleculetype ] > ; Name nrexcl > 1S2 2 > > [ atoms ] > ; nr type resnr resid atom cgnr charge mass > 1 SX 1 1S2 SL 1 0.000 32.0600 > 2 SX 1 1S2 SR 2 0.000 32.0600 > > [ bonds ] > ; ai aj fu c0, c1, ... > 1 2 2 0.2040 5.3E+6 0.2040 5.3E+6 ; SL SR > > > -------------------------------------------------------------------------------------------- > > TRAJ.TRR > ======== > > traj.trr frame 0: > natoms= 2 step= 0 time=0.0000000e+00 lambda= > 0 > box (3x3): > box[ 0]={ 6.37511e+00, 0.00000e+00, 0.00000e+00} > box[ 1]={ 0.00000e+00, 6.37511e+00, 0.00000e+00} > box[ 2]={ 0.00000e+00, 0.00000e+00, 6.37511e+00} > x (2x3): > x[ 0]={ 3.19756e+00, 3.20532e+00, 3.18725e+00} > x[ 1]={ 3.03044e+00, 3.21568e+00, 3.08875e+00} > v (2x3): > v[ 0]={ 2.22763e+00, -2.56083e-01, 1.38905e+00} > v[ 1]={-2.22763e+00, 2.56083e-01, -1.38905e+00} > f (2x3): > f[ 0]={ 3.43615e+03, -2.13216e+02, 2.02509e+03} > f[ 1]={-3.43615e+03, 2.13216e+02, -2.02509e+03} > > > > -------------------------------------------------------------------------------------------- > > MD.LOG > ====== > > > > Input Parameters: > integrator = sd > nsteps = 10000 > init_step = 0 > ns_type = Simple > nstlist = 10 > ndelta = 2 > nstcomm = 1 > comm_mode = Linear > nstlog = 1 > nstxout = 1 > nstvout = 1 > nstfout = 1 > nstenergy = 1 > nstxtcout = 0 > init_t = 0 > delta_t = 0.0001 > xtcprec = 1000 > nkx = 54 > nky = 54 > nkz = 54 > pme_order = 4 > ewald_rtol = 1e-05 > ewald_geometry = 0 > epsilon_surface = 0 > optimize_fft = FALSE > ePBC = xyz > bPeriodicMols = FALSE > bContinuation = FALSE > bShakeSOR = FALSE > etc = No > epc = No > epctype = Isotropic > tau_p = 1 > ref_p (3x3): > ref_p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} > ref_p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} > ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} > compress (3x3): > compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} > compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} > compress[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} > refcoord_scaling = No > posres_com (3): > posres_com[0]= 0.00000e+00 > posres_com[1]= 0.00000e+00 > posres_com[2]= 0.00000e+00 > posres_comB (3): > posres_comB[0]= 0.00000e+00 > posres_comB[1]= 0.00000e+00 > posres_comB[2]= 0.00000e+00 > andersen_seed = 815131 > rlist = 1 > rtpi = 0.05 > coulombtype = PME > rcoulomb_switch = 0 > rcoulomb = 1 > vdwtype = Cut-off > rvdw_switch = 0 > rvdw = 1 > epsilon_r = 1 > epsilon_rf = 1 > tabext = 1 > implicit_solvent = No > gb_algorithm = Still > gb_epsilon_solvent = 80 > nstgbradii = 1 > rgbradii = 2 > gb_saltconc = 0 > gb_obc_alpha = 1 > gb_obc_beta = 0.8 > gb_obc_gamma = 4.85 > sa_surface_tension = 2.092 > DispCorr = No > free_energy = no > init_lambda = 0 > sc_alpha = 0 > sc_power = 0 > sc_sigma = 0.3 > delta_lambda = 0 > nwall = 0 > wall_type = 9-3 > wall_atomtype[0] = -1 > wall_atomtype[1] = -1 > wall_density[0] = 0 > wall_density[1] = 0 > wall_ewald_zfac = 3 > pull = no > disre = No > disre_weighting = Conservative > disre_mixed = FALSE > dr_fc = 1000 > dr_tau = 0 > nstdisreout = 100 > orires_fc = 0 > orires_tau = 0 > nstorireout = 100 > dihre-fc = 1000 > em_stepsize = 0.01 > em_tol = 10 > niter = 20 > fc_stepsize = 0 > nstcgsteep = 1000 > nbfgscorr = 10 > ConstAlg = Lincs > shake_tol = 0.0001 > lincs_order = 4 > lincs_warnangle = 30 > lincs_iter = 1 > bd_fric = 0 > ld_seed = 1993 > cos_accel = 0 > deform (3x3): > deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} > deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} > deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} > userint1 = 0 > userint2 = 0 > userint3 = 0 > userint4 = 0 > userreal1 = 0 > userreal2 = 0 > userreal3 = 0 > userreal4 = 0 > grpopts: > nrdf: 1.5 1.5 > ref_t: 0 0 > tau_t: 0 1 > anneal: No No > ann_npoints: 0 0 > acc: 0 0 0 > nfreeze: N N N > energygrp_flags[ 0]: 0 0 > energygrp_flags[ 1]: 0 0 > efield-x: > n = 0 > efield-xt: > n = 0 > efield-y: > n = 0 > efield-yt: > n = 0 > efield-z: > n = 0 > efield-zt: > n = 0 > bQMMM = FALSE > QMconstraints = 0 > QMMMscheme = 0 > scalefactor = 1 > qm_opts: > ngQM = 0 > Table routines are used for coulomb: TRUE > Table routines are used for vdw: FALSE > Will do PME sum in reciprocal space. > > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ > U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen > A smooth particle mesh Ewald method > J. Chem. Phys. 103 (1995) pp. 8577-8592 > -------- -------- --- Thank You --- -------- -------- > > Using a Gaussian width (1/beta) of 0.320163 nm for Ewald > Cut-off's: NS: 1 Coulomb: 1 LJ: 1 > System total charge: 0.000 > Generated table with 4000 data points for Ewald. > Tabscale = 2000 points/nm > Generated table with 4000 data points for LJ6. > Tabscale = 2000 points/nm > Generated table with 4000 data points for LJ12. > Tabscale = 2000 points/nm > Configuring nonbonded kernels... > Testing x86_64 SSE2 support... present. > > > Removing pbc first time > Center of mass motion removal mode is Linear > We have the following groups for center of mass motion removal: > 0: rest > There are: 2 Atoms > Max number of connections per atom is 1 > Total number of connections is 2 > Max number of graph edges per atom is 1 > Total number of graph edges is 2 > Initial temperature: 17884.7 K > > Started mdrun on node 0 Tue Jun 2 13:38:03 2009 > > Step Time Lambda > 0 0.00000 0.00000 > > Energies (kJ/mol) > G96Bond LJ (SR) Coulomb (SR) Coul. recip. Potential > 1.99416e+01 0.00000e+00 0.00000e+00 0.00000e+00 1.99416e+01 > Kinetic En. Total Energy Temperature Pressure (bar) > nan nan nan nan > > Step Time Lambda > 1 0.00010 0.00000 > > > -- > Inon Sharony > ינון שרוני > +972(3)6407634 > atto.TAU.ac.IL/~inonshar > Please consider your environmental responsibility before printing this > e-mail. > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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