[gmx-users] segfault(11) -- simulation blows up on first step
Justin A. Lemkul
jalemkul at vt.edu
Tue Jun 2 13:22:44 CEST 2009
Inon Sharony 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:
<snip>
> tau_t = 0 1 ; mass/gamma
tau_t for the sd integrator is given in ps^-1; therefore a value of zero could
be causing the sd integrator to use some sort of infinite friction coefficient.
If you are trying to use tau_t = 0 to turn off temperature coupling, it may not
work with sd (not sure), or it could be causing some physically unrealistic
condition. Why would two bonded atoms experience different temperatures or
coupling/lack thereof?
-Justin
> 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.
>
>
> ------------------------------------------------------------------------
>
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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