[gmx-users] core dumped during equilibration in gromacs
ISHRAT JAHAN
jishrat17 at gmail.com
Wed Mar 22 11:07:37 CET 2017
I have reduced the force and timestep as given at http://www.gromacs.org/
Documentation/Terminology/Blowing_Up
<http://www.gromacs.org/Documentation/Terminology/Blowing_Up> but still
getting an error like-
Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)
writing lowest energy coordinates.
Back Off! I just backed up prion_em.gro to ./#prion_em.gro.1#
Steepest Descents converged to machine precision in 726 steps,
but did not reach the requested Fmax < 1000.
Potential Energy = -1.7322245e+05
Maximum force = 8.0706294e+03 on atom 2216
Norm of force = 1.4435008e+02
if i proceed for pr with this result segmentation fault occured again.
On Wed, Mar 22, 2017 at 3:00 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:
> Hi,
>
> Your initial structure seems to be horribly broken, e.g. clashing atoms.
> Consider the advice at
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up
>
> Mark
>
> On Wed, Mar 22, 2017 at 10:27 AM ISHRAT JAHAN <jishrat17 at gmail.com> wrote:
>
> > Dear all,
> > I am trying to simulate protein in urea box using "amber99sb-ildn" force
> > field.when i do the energy minimization step with emtol 1000 it shows
> many
> > lincs warning then i increase the emtol to 1500 minimization occur in 1
> > step but in pr run it shows segmentation fault as-
> > step 13: Water molecule starting at atom 12818 can not be settled.
> > Check for bad contacts and/or reduce the timestep if appropriate.
> > 1909 1911 90.5 0.1010 6.9898 0.1010
> > 1843 1845 90.1 0.1335 0.7170 0.1335
> > 2426 2424 89.0 0.1010 1.3001 0.1010
> > 3834 3832 30.3 0.1011 0.1011 0.1010
> > 3975 3973 90.8 0.1020 3.5240 0.1010
> > 3974 3973 93.5 0.1037 0.6352 0.1010
> > 1845 1847 89.5 0.1010 1.1038 0.1010
> > 2425 2424 89.4 0.1010 2.2398 0.1010
> > 3840 3842 86.6 0.1010 0.4727 0.1010
> > 3840 3841 72.6 0.1010 0.0943 0.1010
> > 4302 4301 39.8 0.1010 0.1010 0.1010
> > 1845 1846 89.9 0.1010 2.4267 0.1010
> > 3020 3019 89.0 0.1229 2.5234 0.1229
> > 1909 1910 90.5 0.1010 7.4258 0.1010
> > 3723 3724 88.8 0.1229 0.2757 0.1229
> > 4348 4347 89.5 0.1229 0.6861 0.1229
> > 1850 1848 90.0 0.1010 2.6093 0.1010
> > 3024 3019 87.5 0.1335 1.4130 0.1335
> > 1912 1914 92.9 0.1010 1.9229 0.1010
> > 3723 3728 40.0 0.1335 0.1390 0.1335
> > 4352 4347 89.0 0.1335 0.5260 0.1335
> > 1849 1848 90.0 0.1010 2.2107 0.1010
> > 3021 3019 89.4 0.1335 2.6444 0.1335
> > 3080 3075 62.9 0.1336 0.1403 0.1335
> > 3082 3080 88.5 0.1011 0.1289 0.1010
> > 3081 3080 89.9 0.1011 1.6887 0.1010
> > 4349 4347 85.8 0.1341 0.0908 0.1335
> > 1843 1848 89.2 0.1335 0.7476 0.1335
> > 3023 3021 89.4 0.1010 5.1859 0.1010
> > 3728 3730 90.1 0.1010 2.8064 0.1010
> > 3728 3729 90.3 0.1010 1.1145 0.1010
> > 3723 3725 95.0 0.1335 0.1466 0.1335
> > 3725 3727 89.7 0.1010 2.5135 0.1010
> > 3725 3726 89.5 0.1010 1.5862 0.1010
> > 3913 3912 78.0 0.2808 0.1013 0.1010
> > 4127 4125 90.0 0.1010 3.2749 0.1010
> > 4126 4125 90.0 0.1010 3.4106 0.1010
> > 3078 3077 71.1 0.1007 0.0834 0.1010
> > 1847 1845 89.5 0.1010 1.1038 0.1010
> > 1846 1845 89.9 0.1010 2.4267 0.1010
> > 3348 3347 31.4 0.1229 0.1454 0.1229
> > 3349 3347 86.4 0.1335 0.2715 0.1335
> > 3351 3349 90.0 0.1010 3.8643 0.1010
> > 4354 4352 89.9 0.1010 1.4920 0.1010
> > 3022 3021 69.0 0.1010 0.1722 0.1010
> >
> > step 13: Water molecule starting at atom 19622 can not be settled.
> > Check for bad contacts and/or reduce the timestep if appropriate.
> > 2378 2376 89.7 0.1010 1.7581 0.1010
> > 3350 3349 89.9 0.1010 0.4917 0.1010
> > 4353 4352 89.9 0.1010 2.7233 0.1010
> > 3026 3024 120.8 0.1010 3.7674 0.1010
> > 2377 2376 89.9 0.1008 3.4398 0.1010
> > 3324 3323 95.3 0.1229 0.2979 0.1229
> > 3323 3328 60.3 0.1335 0.1799 0.1335
> > 3025 3024 89.8 0.1010 3.2735 0.1010
> > 2371 2376 87.9 0.1336 0.6651 0.1335
> > 3972 3971 88.6 0.1416 2.6683 0.1229
> > 3976 3971 82.7 0.2058 16.5778 0.1335
> > 3973 3971 94.1 0.1492 2.8224 0.1335
> > 3978 3976 76.6 0.1818 16.0156 0.1010
> > 3977 3976 90.0 5.4502 248.0255 0.1010
> > 4351 4349 89.7 0.1060 1.6853 0.1010
> > 2372 2371 89.7 0.1229 1.2811 0.1229
> > 2371 2372 89.7 0.1229 1.2811 0.1229
> > 3328 3330 90.4 0.1010 2.4729 0.1010
> > 3328 3329 90.3 0.1010 3.4044 0.1010
> > 2371 2376 87.9 0.1336 0.6651 0.1335
> > 2371 2373 89.0 0.1335 1.0416 0.1335
> > 4350 4349 89.8 0.1013 2.1256 0.1010
> > 3327 3325 93.4 0.1010 0.4147 0.1010
> > 2376 2378 89.7 0.1010 1.7581 0.1010
> > 2373 2375 89.6 0.1011 2.9293 0.1010
> > 3234 3232 89.9 0.1010 3.5885 0.1010
> > 3233 3232 89.9 0.1010 3.0155 0.1010
> > 3227 3232 89.1 0.1335 0.7809 0.1335
> > 3227 3228 87.5 0.1229 0.1716 0.1229
> > 3227 3229 87.3 0.1335 0.2695 0.1335
> > 3229 3231 89.3 0.1010 0.6305 0.1010
> > 3229 3230 89.8 0.1010 1.9634 0.1010
> > 4305 4304 32.9 0.1008 0.1009 0.1010
> > 3561 3560 34.3 0.1010 0.1010 0.1010
> > 3836 3835 86.5 0.1229 0.5365 0.1229
> > 3840 3835 88.6 0.1335 1.1454 0.1335
> > 3835 3837 88.6 0.1335 1.2985 0.1335
> > 3837 3839 88.6 0.1010 0.8127 0.1010
> > 3837 3838 88.2 0.1010 0.6595 0.1010
> > 3723 3724 88.8 0.1229 0.2757 0.1229
> > 3728 3723 40.0 0.1335 0.1390 0.1335
> > 3725 3723 95.0 0.1335 0.1466 0.1335
> > 3727 3725 89.7 0.1010 2.5135 0.1010
> > 3726 3725 89.5 0.1010 1.5862 0.1010
> > 3730 3728 90.1 0.1010 2.8064 0.1010
> > 3729 3728 90.3 0.1010 1.1145 0.1010
> > 3740 3739 89.4 0.1229 0.8769 0.1229
> > 2376 2377 89.9 0.1008 3.4398 0.1010
> > 2373 2374 89.9 0.1010 3.1833 0.1010
> > 3326 3325 90.8 0.1010 1.8066 0.1010
> > 3744 3739 89.9 0.1335 2.8404 0.1335
> > 2373 2371 89.0 0.1335 1.0416 0.1335
> > 1908 1907 92.0 0.1229 3.3603 0.1229
> > 3449 3448 90.0 0.1044 0.1239 0.1010
> > 3741 3739 87.2 0.1335 0.9979 0.1335
> > 2375 2373 89.6 0.1011 2.9293 0.1010
> > 1912 1907 92.1 0.1335 3.2085 0.1335
> > 3228 3227 87.5 0.1229 0.1716 0.1229
> > 3227 3232 89.1 0.1335 0.7809 0.1335
> > 3743 3741 90.2 0.1010 1.9862 0.1010
> > 1909 1907 92.4 0.1335 2.8016 0.1335
> > 2374 2373 89.9 0.1010 3.1833 0.1010
> > 3232 3234 89.9 0.1010 3.5885 0.1010
> > 3232 3233 89.9 0.1010 3.0155 0.1010
> > 3229 3227 87.3 0.1335 0.2695 0.1335
> > 3231 3229 89.3 0.1010 0.6305 0.1010
> > 3230 3229 89.8 0.1010 1.9634 0.1010
> > 3560 3561 34.3 0.1010 0.1010 0.1010
> > 3172 3171 89.1 0.1229 1.8214 0.1229
> > 3176 3171 90.9 0.1335 3.6835 0.1335
> > 3173 3171 86.8 0.1335 1.7813 0.1335
> > 3175 3173 99.7 0.1010 0.3723 0.1010
> > 3174 3173 92.0 0.1010 1.8602 0.1010
> > 3178 3176 89.6 0.1010 13.5133 0.1010
> > 3177 3176 88.3 0.1010 2.6361 0.1010
> > 3490 3488 61.1 0.1019 0.1001 0.1010
> > 3506 3504 62.3 0.1001 0.1020 0.1010
> > 3116 3115 88.8 0.1229 0.4402 0.1229
> > 3120 3115 90.0 0.1335 0.5524 0.1335
> > 3117 3115 82.8 0.1335 0.2489 0.1335
> > 3119 3117 31.8 0.1010 0.1259 0.1010
> > 3118 3117 34.5 0.1010 0.1223 0.1010
> > 3122 3120 85.9 0.1010 0.2776 0.1010
> > 3121 3120 119.1 0.1010 3.5355 0.1010
> > 3589 3590 37.2 0.0995 0.1009 0.1010
> > 3592 3594 76.3 0.2306 0.1015 0.1010
> >
> > step 13: Water molecule starting at atom 15707 can not be settled.
> > Check for bad contacts and/or reduce the timestep if appropriate.
> > 3742 3741 90.3 0.1010 1.3761 0.1010
> > 1911 1909 90.5 0.1010 6.9898 0.1010
> > 2820 2819 93.6 0.1229 0.1882 0.1229
> > 3842 3840 86.6 0.1010 0.4727 0.1010
> > 1910 1909 90.5 0.1010 7.4258 0.1010
> > 2824 2819 89.7 0.1335 0.3039 0.1335
> > 3841 3840 72.6 0.1010 0.0943 0.1010
> > 1912 1914 92.9 0.1010 1.9229 0.1010
> > 2821 2819 84.6 0.1335 0.1386 0.1335
> > 1923 1924 38.9 0.1229 0.1316 0.1229
> > 1912 1913 95.5 0.1010 1.0391 0.1010
> > 4004 4003 89.2 0.1229 0.6499 0.1229
> > 1923 1925 32.8 0.1335 0.1338 0.1335
> > 2713 2712 78.7 0.1019 0.1004 0.1010
> > 4008 4003 88.4 0.1335 0.2378 0.1335
> > 1925 1927 89.9 0.1010 1.7174 0.1010
> > 2709 2711 47.8 0.1006 0.1009 0.1010
> > 3330 3328 90.4 0.1010 2.4729 0.1010
> > 3329 3328 90.3 0.1010 3.4044 0.1010
> > 3323 3328 60.3 0.1335 0.1799 0.1335
> > 3323 3324 95.3 0.1229 0.2979 0.1229
> > 3325 3327 93.4 0.1010 0.4147 0.1010
> > 3325 3326 90.8 0.1010 1.8066 0.1010
> > 4005 4003 88.5 0.1335 0.7968 0.1335
> > 1925 1926 89.1 0.1010 0.0985 0.1010
> >
> > step 13: Water molecule starting at atom 4667 can not be settled.
> > Check for bad contacts and/or reduce the timestep if appropriate.
> > 4007 4005 89.9 0.1010 1.6885 0.1010
> > 2712 2713 78.7 0.1019 0.1004 0.1010
> > 2711 2709 47.8 0.1006 0.1009 0.1010
> > 2826 2824 104.1 0.1010 0.2124 0.1010
> > 2825 2824 91.4 0.1010 2.1142 0.1010
> > 4006 4005 90.0 0.1010 2.8577 0.1010
> > 4010 4008 89.7 0.1010 3.8945 0.1010
> > 4009 4008 89.3 0.1010 1.3050 0.1010
> > 3772 3771 89.6 0.1229 0.7077 0.1229
> >
> > step 13: Water molecule starting at atom 11183 can not be settled.
> > Check for bad contacts and/or reduce the timestep if appropriate.
> > 3776 3771 89.0 0.1335 0.5022 0.1335
> > 3773 3771 86.2 0.1335 0.3640 0.1335
> > 3778 3776 89.8 0.1010 3.6930 0.1010
> > 3777 3776 88.9 0.1009 0.1931 0.1010
> > 4172 4171 68.6 0.1229 0.1187 0.1229
> > 4176 4171 91.0 0.1335 0.2675 0.1335
> > 4173 4171 89.6 0.1335 0.2976 0.1335
> > 4175 4173 90.0 0.1010 3.2713 0.1010
> > 4174 4173 90.0 0.1010 2.6987 0.1010
> > 4178 4176 89.6 0.1010 0.5865 0.1010
> > 4177 4176 89.9 0.1010 3.6148 0.1010
> > 3746 3744 89.4 0.1010 2.3745 0.1010
> > 3745 3744 89.7 0.1010 5.5164 0.1010
> > 4248 4243 92.0 0.1335 0.8513 0.1335
> > 4245 4243 90.2 0.1335 1.1166 0.1335
> > 4250 4248 90.0 0.1010 4.1474 0.1010
> > 4249 4248 90.1 0.1010 3.4663 0.1010
> > 3852 3851 94.8 0.1229 0.3110 0.1229
> > 3856 3851 87.7 0.1335 0.2355 0.1335
> > 3853 3851 98.2 0.1335 0.3382 0.1335
> > 3855 3853 43.3 0.1010 3.6650 0.1010
> > 3854 3853 88.2 0.1010 0.3390 0.1010
> > 3858 3856 108.0 0.1010 0.1709 0.1010
> > 4247 4245 90.7 0.1010 1.3392 0.1010
> > 4246 4245 90.5 0.1010 1.8016 0.1010
> >
> > step 13: Water molecule starting at atom 18938 can not be settled.
> > Check for bad contacts and/or reduce the timestep if appropriate.
> > Wrote pdb files with previous and current coordinates
> > Wrote pdb files with previous and current coordinates
> > Wrote pdb files with previous and current coordinates
> > Wrote pdb files with previous and current coordinates
> > Wrote pdb files with previous and current coordinates
> > Wrote pdb files with previous and current coordinates
> > Segmentation fault (core dumped)
> >
> > Here is my em.mdp and pr_nvt.mdp file-
> > ;^M
> > ; User spoel (236)^M
> > ; Wed Nov 3 17:12:44 1993^M
> > ; Input file^M
> > ;^M
> > cpp = /usr/bin/cpp^M
> > define = -DFLEX_SPC^M
> > constraints = all-bonds
> > integrator = steep ^M
> > nsteps = 50000
> > ; Energy minimizing stuff^M
> > emtol = 1500^M
> > emstep = 0.01^M
> > nstlist = 1^M
> > nstcomm = 100^M
> > ns_type = grid^M
> > rlist = 0.8 ^M
> > coulombtype = PME^M
> > rcoulomb = 0.8^M
> > rvdw = 0.8
> > pbc = xyz
> > fourierspacing = 0.12^M
> > fourier_nx = 0^M
> > fourier_ny = 0^M
> > fourier_nz = 0^M
> > pme_order = 4^M
> > ewald_rtol = 1e-5^M
> > optimize_fft = yes^M
> > Tcoupl = no^M
> > Pcoupl = no^M
> > gen_vel = no^M
> > ~
> > PR_NVT.MDP-
> > ;^M
> > ; User spoel (236)^M
> > ; Wed Nov 3 17:12:44 1993^M
> > ; Input file^M
> > ;^M
> > title = Yo^M
> > cpp = /usr/bin/cpp^M
> > define = -DPOSRES^M
> > constraints = all-bonds^M
> > constraintalgorithm = LINCS^M
> > integrator = md^M
> > dt = 0.002 ; ps !^M
> > nsteps = 50000 ; total 10 ps.^M
> > nstcomm = 1000^M
> > nstxout = 1000^M
> > nstvout = 1000^M
> > nstfout = 0^M
> > nstlog = 10^M
> > nstenergy = 10^M
> > nstlist = 10^M
> > ns_type = grid^M
> > rlist = 0.8
> > coulombtype = PME^M
> > rcoulomb = 0.8
> > rvdw = 0.8
> > fourierspacing = 0.12^M
> > fourier_nx = 0^M
> > fourier_ny = 0^M
> > fourier_nz = 0^M
> > pme_order = 4^M
> > ewald_rtol = 1e-5^M
> > optimize_fft = yes^M
> > ; Berendsen temperature coupling is on in two groups^M
> > Tcoupl = V-rescale^M
> > tc-grps = System ^M
> > tau_t = 0.1 ^M
> > ref_t = 300 ^M
> > ; Energy monitoring^M
> > energygrps = System^M
> > ; Pressure coupling is off^M
> >
> > Please help me to get out of this .
> > Thanks in advance.
> > --
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