It happens immediately at step 0., and the log file looks like :<br><br><br><br>Input Parameters:<br> integrator = md<br> nsteps = 20000<br> init_step = 0<br> ns_type = Grid<br>
nstlist = 10<br> ndelta = 2<br> nstcomm = 0<br> comm_mode = Linear<br> nstlog = 1000<br> nstxout = 600<br> nstvout = 600<br>
nstfout = 600<br> nstenergy = 1000<br> nstxtcout = 1000<br> init_t = 0<br> delta_t = 0.001<br> xtcprec = 10000<br> nkx = 44<br>
nky = 42<br> nkz = 120<br> pme_order = 4<br> ewald_rtol = 1e-05<br> ewald_geometry = 1<br> epsilon_surface = -1<br> optimize_fft = FALSE<br>
ePBC = xyz<br> bPeriodicMols = FALSE<br> bContinuation = FALSE<br> bShakeSOR = FALSE<br> etc = Nose-Hoover<br> epc = No<br> epctype = Isotropic<br>
tau_p = 1<br> ref_p (3x3):<br> ref_p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br> ref_p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br> ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br>
compress (3x3):<br> compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br> compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br> compress[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br>
refcoord_scaling = No<br> posres_com (3):<br> posres_com[0]= 0.00000e+00<br> posres_com[1]= 0.00000e+00<br> posres_com[2]= 0.00000e+00<br> posres_comB (3):<br> posres_comB[0]= 0.00000e+00<br>
posres_comB[1]= 0.00000e+00<br> posres_comB[2]= 0.00000e+00<br> andersen_seed = 815131<br> rlist = 1.1<br> rtpi = 0.05<br> coulombtype = PME<br> rcoulomb_switch = 0<br>
rcoulomb = 1.1<br> vdwtype = Cut-off<br> rvdw_switch = 0<br> rvdw = 1.1<br> epsilon_r = 1<br> epsilon_rf = 1<br> tabext = 1<br>
implicit_solvent = No<br> gb_algorithm = Still<br> gb_epsilon_solvent = 80<br> nstgbradii = 1<br> rgbradii = 2<br> gb_saltconc = 0<br> gb_obc_alpha = 1<br>
gb_obc_beta = 0.8<br> gb_obc_gamma = 4.85<br> sa_surface_tension = 2.092<br> DispCorr = EnerPres<br> free_energy = no<br> init_lambda = 0<br> sc_alpha = 0<br>
sc_power = 0<br> sc_sigma = 0.3<br> delta_lambda = 0<br> nwall = 0<br> wall_type = 9-3<br> wall_atomtype[0] = -1<br> wall_atomtype[1] = -1<br>
wall_density[0] = 0<br> wall_density[1] = 0<br> wall_ewald_zfac = 3<br> pull = no<br> disre = No<br> disre_weighting = Conservative<br> disre_mixed = FALSE<br>
dr_fc = 1000<br> dr_tau = 0<br> nstdisreout = 100<br> orires_fc = 0<br> orires_tau = 0<br> nstorireout = 100<br> dihre-fc = 1000<br>
em_stepsize = 0.01<br> em_tol = 100<br> niter = 20<br> fc_stepsize = 0<br> nstcgsteep = 1000<br> nbfgscorr = 10<br> ConstAlg = Lincs<br>
shake_tol = 0.0001<br> lincs_order = 4<br> lincs_warnangle = 30<br> lincs_iter = 1<br> bd_fric = 0<br> ld_seed = 1993<br> cos_accel = 0<br>
deform (3x3):<br> deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br> deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br> deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br> userint1 = 0<br>
userint2 = 0<br> userint3 = 0<br> userint4 = 0<br> userreal1 = 0<br> userreal2 = 0<br> userreal3 = 0<br> userreal4 = 0<br>grpopts:<br>
nrdf: 0 12822<br> ref_t: 0 300<br> tau_t: 0 0.2<br>anneal: No No<br>ann_npoints: 0 0<br> acc: 0 0 0<br>
nfreeze: Y Y Y N N N<br> energygrp_flags[ 0]: 1 0<br> energygrp_flags[ 1]: 0 0<br> efield-x:<br> n = 0<br> efield-xt:<br> n = 0<br> efield-y:<br>
n = 0<br> efield-yt:<br> n = 0<br> efield-z:<br> n = 0<br> efield-zt:<br> n = 0<br> bQMMM = FALSE<br> QMconstraints = 0<br> QMMMscheme = 0<br> scalefactor = 1<br>
qm_opts:<br> ngQM = 0<br>Table routines are used for coulomb: TRUE<br>Table routines are used for vdw: FALSE<br>Will do PME sum in reciprocal space.<br><br>++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++<br>
U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen <br>A smooth particle mesh Ewald method<br>J. Chem. Phys. 103 (1995) pp. 8577-8592<br>-------- -------- --- Thank You --- -------- --------<br><br>
Using the Ewald3DC correction for systems with a slab geometry.<br><br>++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++<br>Y. In-Chul and M. L. Berkowitz<br>Ewald summation for systems with slab geometry<br>J. Chem. Phys. 111 (1999) pp. 3155-3162<br>
-------- -------- --- Thank You --- -------- --------<br><br>Using a Gaussian width (1/beta) of 0.352179 nm for Ewald<br>Cut-off's: NS: 1.1 Coulomb: 1.1 LJ: 1.1<br>System total charge: 0.000<br>Generated table with 4200 data points for Ewald.<br>
Tabscale = 2000 points/nm<br>Generated table with 4200 data points for LJ6.<br>Tabscale = 2000 points/nm<br>Generated table with 4200 data points for LJ12.<br>Tabscale = 2000 points/nm<br><br>Enabling SPC water optimization for 2137 molecules.<br>
<br>Configuring nonbonded kernels...<br>Testing ia32 SSE2 support... present.<br><br><br>Removing pbc first time<br><br>++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++<br>S. Miyamoto and P. A. Kollman<br>SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid<br>
Water Models<br>J. Comp. Chem. 13 (1992) pp. 952-962<br>-------- -------- --- Thank You --- -------- --------<br><br>There are: 7699 Atoms<br>Max number of connections per atom is 2<br>Total number of connections is 8548<br>
Max number of graph edges per atom is 2<br>Total number of graph edges is 8548<br><br>Constraining the starting coordinates (step 0)<br><br>Constraining the coordinates at t0-dt (step 0)<br>RMS relative constraint deviation after constraining: 0.00e+00<br>
Initial temperature: 304.27 K<br><br>Started mdrun on node 0 Thu May 20 16:33:38 2010<br><br> Step Time Lambda<br> 0 0.00000 0.00000<br><br>Grid: 5 x 5 x 14 cells<br>
Long Range LJ corr.: <C6> 1.1930e-03<br>Long Range LJ corr.: Epot -415.301, Pres: -51.4754, Vir: 415.301<br> Energies (kJ/mol)<br> LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential<br>
6.44979e+04 -4.15301e+02 -1.00185e+05 -4.94669e+03 -4.10490e+04<br> Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)<br> 1.72141e+04 -2.38349e+04 -2.38347e+04 3.22940e+02 1.36187e+04<br>
<br><br><div class="gmail_quote">On Thu, May 20, 2010 at 4:30 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div><div></div><div class="h5"><br>
<br>
Sikandar Mashayak wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi<br>
<br>
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.<br>
<br>
So what could be the source of segmentation fault?<br>
<br>
</blockquote>
<br></div></div>
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.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
thanks<br>
sikandar<br>
<br>
</blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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