[gmx-users] mdrun segmentation fault
Justin A. Lemkul
jalemkul at vt.edu
Thu May 20 23:59:37 CEST 2010
Sikandar Mashayak wrote:
> It happens immediately at step 0., and the log file looks like :
>
>
That suggests to me that the system is inherently unstable, which can occur for
a variety of reasons.
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
A few more comments below.
>
> Input Parameters:
> integrator = md
> nsteps = 20000
> init_step = 0
> ns_type = Grid
> nstlist = 10
> ndelta = 2
> nstcomm = 0
> comm_mode = Linear
> nstlog = 1000
> nstxout = 600
> nstvout = 600
> nstfout = 600
> nstenergy = 1000
> nstxtcout = 1000
> init_t = 0
> delta_t = 0.001
> xtcprec = 10000
> nkx = 44
> nky = 42
> nkz = 120
> pme_order = 4
> ewald_rtol = 1e-05
> ewald_geometry = 1
> epsilon_surface = -1
> optimize_fft = FALSE
> ePBC = xyz
> bPeriodicMols = FALSE
> bContinuation = FALSE
> bShakeSOR = FALSE
> etc = Nose-Hoover
> 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 = 1.1
> rtpi = 0.05
> coulombtype = PME
> rcoulomb_switch = 0
> rcoulomb = 1.1
> vdwtype = Cut-off
> rvdw_switch = 0
> rvdw = 1.1
> 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 = EnerPres
> 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 = 100
> 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: 0 12822
> ref_t: 0 300
> tau_t: 0 0.2
> anneal: No No
> ann_npoints: 0 0
> acc: 0 0 0
> nfreeze: Y Y Y N
> N N
> energygrp_flags[ 0]: 1 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 the Ewald3DC correction for systems with a slab geometry.
>
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> Y. In-Chul and M. L. Berkowitz
> Ewald summation for systems with slab geometry
> J. Chem. Phys. 111 (1999) pp. 3155-3162
> -------- -------- --- Thank You --- -------- --------
>
> Using a Gaussian width (1/beta) of 0.352179 nm for Ewald
> Cut-off's: NS: 1.1 Coulomb: 1.1 LJ: 1.1
> System total charge: 0.000
> Generated table with 4200 data points for Ewald.
> Tabscale = 2000 points/nm
> Generated table with 4200 data points for LJ6.
> Tabscale = 2000 points/nm
> Generated table with 4200 data points for LJ12.
> Tabscale = 2000 points/nm
>
> Enabling SPC water optimization for 2137 molecules.
>
> Configuring nonbonded kernels...
> Testing ia32 SSE2 support... present.
>
>
> Removing pbc first time
>
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> S. Miyamoto and P. A. Kollman
> SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
> Water Models
> J. Comp. Chem. 13 (1992) pp. 952-962
> -------- -------- --- Thank You --- -------- --------
>
> There are: 7699 Atoms
> Max number of connections per atom is 2
> Total number of connections is 8548
> Max number of graph edges per atom is 2
> Total number of graph edges is 8548
>
> Constraining the starting coordinates (step 0)
>
> Constraining the coordinates at t0-dt (step 0)
> RMS relative constraint deviation after constraining: 0.00e+00
> Initial temperature: 304.27 K
>
> Started mdrun on node 0 Thu May 20 16:33:38 2010
>
> Step Time Lambda
> 0 0.00000 0.00000
>
> Grid: 5 x 5 x 14 cells
> Long Range LJ corr.: <C6> 1.1930e-03
> Long Range LJ corr.: Epot -415.301, Pres: -51.4754, Vir: 415.301
> Energies (kJ/mol)
> LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
> 6.44979e+04 -4.15301e+02 -1.00185e+05 -4.94669e+03 -4.10490e+04
> Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
> 1.72141e+04 -2.38349e+04 -2.38347e+04 3.22940e+02 1.36187e+04
>
Here's where I see the biggest problems. Your actual temperature is far greater
than the desired reference temperature, and the pressure is astronomical. These
to facts suggest that your system is shearing apart. Is this the first MD for
this system? Have you done prior equilibration? If you haven't stably
minimized and equilibrated the system, using the N-H thermostat is a bad idea.
The temperature of a system that is far from equilibrium will fluctuate
unpredictably using N-H. It is better to use a weak coupling scheme (i.e.
Berendsen or V-rescale) to equilibrate the system, then switch to N-H for data
collection.
Other than that, see the diagnostic tips at the link above.
-Justin
>
> On Thu, May 20, 2010 at 4:30 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> Sikandar Mashayak wrote:
>
> Hi
>
> I have gromacs input files for md simulation, with these set up
> files (*.mdp,*.top,*.itp *.gro), I can successfully run grompp
> and mdrun on one machine, but when I move it to other machine, I
> get segmentation fault when I do mdrun. Both the machines have
> exactly same types of installation of gromacs 4.0.7 . Also, I
> can run water tutorials successfully on both the machines.
>
> So what could be the source of segmentation fault?
>
>
> MD is chaotic, so you may not get the same result every time you run
> a simulation. Since you've not said how quickly the seg fault
> occurs it is exceptionally hard to diagnose. Generally, seg faults
> with mdrun occur because the system crashes from an instability.
> Without substantially more information (system contents, .mdp
> settings, relevant log file output, etc) there is not much more to
> suggest.
>
> -Justin
>
> thanks
> sikandar
>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at 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-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
More information about the gromacs.org_gmx-users
mailing list