Re: [gmx-users] Signal: Segmentation faul
shikha agarwal wrote: hi, HAPPY NEW YEAR I am experiencing a segmentation fault during mdrun in equlibration step . error Wrote pdb files with previous and current coordinates [shikha-desktop:01719] *** Process received signal *** [shikha-desktop:01719] Signal: Segmentation fault (11) [shikha-desktop:01719] Signal code: Address not mapped (1) [shikha-desktop:01719] Failing at address: 0x8d22a70 [shikha-desktop:01719] [ 0] [0xb87410] [shikha-desktop:01719] [ 1] mdrun(do_nonbonded+0x769) [0x82a9789] [shikha-desktop:01719] *** End of error message *** Segmentation fault bottom lines of my .log file after energy minimization is this Step Time Lambda 1135711357.00.0 Step Time Lambda 1135811358.00.0 Step Time Lambda 1135911359.00.0 Step Time Lambda 1136011360.00.0 Step Time Lambda 1136111361.00.0 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 1000 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) Steepest Descents converged to machine precision in 11362 steps, but did not reach the requested Fmax < 1000. Potential Energy = -5.4871900e+06 Maximum force = 3.9830833e+03 on atom 4511 Norm of force = 1.9521437e+01 Well, EM completed, but the forces are still very high, indicating that the system is likely not yet stable. Look at the structure to see what might be causing problems around atom 4511. -Justin -- 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Signal: Segmentation faul
Your log file does indicate that the steepest descent converged. I dont know why you have the error messages. Why not go ahead with MD ? Amit On Sun, Jan 2, 2011 at 10:35 PM, shikha agarwal wrote: > hi, > HAPPY NEW YEAR > > I am experiencing a segmentation fault during mdrun in equlibration step . > error > > Wrote pdb files with previous and current coordinates > [shikha-desktop:01719] *** Process received signal *** > [shikha-desktop:01719] Signal: Segmentation fault (11) > [shikha-desktop:01719] Signal code: Address not mapped (1) > [shikha-desktop:01719] Failing at address: 0x8d22a70 > [shikha-desktop:01719] [ 0] [0xb87410] > [shikha-desktop:01719] [ 1] mdrun(do_nonbonded+0x769) [0x82a9789] > [shikha-desktop:01719] *** End of error message *** > Segmentation fault > > > > > > bottom lines of my .log file after energy minimization is this > > > > Step Time Lambda > 1135711357.00.0 > >Step Time Lambda > 1135811358.00.0 > >Step Time Lambda > 1135911359.00.0 > >Step Time Lambda > 1136011360.00.0 > >Step Time Lambda > 1136111361.00.0 > > > Stepsize too small, or no change in energy. > Converged to machine precision, > but not to the requested precision Fmax < 1000 > > 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) > > Steepest Descents converged to machine precision in 11362 steps, > but did not reach the requested Fmax < 1000. > Potential Energy = -5.4871900e+06 > Maximum force = 3.9830833e+03 on atom 4511 > Norm of force = 1.9521437e+01 > > M E G A - F L O P S A C C O U N T I N G > >RF=Reaction-Field FE=Free Energy SCFE=Soft-Core/Free Energy >T=TabulatedW3=SPC/TIP3pW4=TIP4p (single or pairs) >NF=No Forces > > Computing: M-Number M-Flops % Flops > > - > LJ 10523.695513 347281.952 0.4 > Coul(T) 6405.625131 269036.256 0.3 > Coul(T) [W3] 226.446553 28305.819 0.0 > Coul(T) + LJ 4637.739866 255075.693 0.3 > Coul(T) + LJ [W3] 1706.661036 235519.223 0.3 > Coul(T) + LJ [W3-W3]141595.84421154089612.48969.1 > Outer nonbonded loop 18947.604080 189476.041 0.2 > 1,4 nonbonded interactions 105.1893969467.046 0.0 > Calc Weights 11755.000218 423180.008 0.5 > Spread Q Bspline250773.337984 501546.676 0.6 > Gather F Bspline250773.337984 1504640.028 1.9 > 3D-FFT 1217431.505524 9739452.04412.4 > Solve PME14842.953216 949949.006 1.2 > NS-Pairs418574.562328 8790065.80911.2 > Reset In Box 1338.8867184016.660 0.0 > Shift-X 3916.765450 23500.593 0.0 > CG-CoM3918.333406 11755.000 0.0 > Bonds 114.1312906733.746 0.0 > Angles 142.695358 23972.820 0.0 > Propers102.167104 23396.267 0.0 > Impropers 28.9844626028.768 0.0 > RB-Dihedrals 2.885948 712.829 0.0 > Pos. Restr. 38.1990441909.952 0.0 > Virial3918.844696 70539.205 0.1 > Settle2534.725856 818716.451 1.0 > > - > Total78323890.379 100.0 > > - > > > R E A L C Y C L E A N D T I M E A C C O U N T I N G > > Computing: Nodes Number G-CyclesSeconds % > --- > Neighbor search1 1136230337.457 6067.718.8 > Force 1 1136235859.263 7172.122.3 > PME mesh 1 1136212486.060 2497.3 7.8 > Constraints1 22723 1294.000 258.8 0.8 > Rest 1 81096.73016219.8
[gmx-users] Signal: Segmentation faul
hi, HAPPY NEW YEAR I am experiencing a segmentation fault during mdrun in equlibration step . error Wrote pdb files with previous and current coordinates [shikha-desktop:01719] *** Process received signal *** [shikha-desktop:01719] Signal: Segmentation fault (11) [shikha-desktop:01719] Signal code: Address not mapped (1) [shikha-desktop:01719] Failing at address: 0x8d22a70 [shikha-desktop:01719] [ 0] [0xb87410] [shikha-desktop:01719] [ 1] mdrun(do_nonbonded+0x769) [0x82a9789] [shikha-desktop:01719] *** End of error message *** Segmentation fault bottom lines of my .log file after energy minimization is this Step Time Lambda 1135711357.00.0 Step Time Lambda 1135811358.00.0 Step Time Lambda 1135911359.00.0 Step Time Lambda 1136011360.00.0 Step Time Lambda 1136111361.00.0 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 1000 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) Steepest Descents converged to machine precision in 11362 steps, but did not reach the requested Fmax < 1000. Potential Energy = -5.4871900e+06 Maximum force = 3.9830833e+03 on atom 4511 Norm of force = 1.9521437e+01 M E G A - F L O P S A C C O U N T I N G RF=Reaction-Field FE=Free Energy SCFE=Soft-Core/Free Energy T=TabulatedW3=SPC/TIP3pW4=TIP4p (single or pairs) NF=No Forces Computing: M-Number M-Flops % Flops - LJ 10523.695513 347281.952 0.4 Coul(T) 6405.625131 269036.256 0.3 Coul(T) [W3] 226.446553 28305.819 0.0 Coul(T) + LJ 4637.739866 255075.693 0.3 Coul(T) + LJ [W3] 1706.661036 235519.223 0.3 Coul(T) + LJ [W3-W3]141595.84421154089612.48969.1 Outer nonbonded loop 18947.604080 189476.041 0.2 1,4 nonbonded interactions 105.1893969467.046 0.0 Calc Weights 11755.000218 423180.008 0.5 Spread Q Bspline250773.337984 501546.676 0.6 Gather F Bspline250773.337984 1504640.028 1.9 3D-FFT 1217431.505524 9739452.04412.4 Solve PME14842.953216 949949.006 1.2 NS-Pairs418574.562328 8790065.80911.2 Reset In Box 1338.8867184016.660 0.0 Shift-X 3916.765450 23500.593 0.0 CG-CoM3918.333406 11755.000 0.0 Bonds 114.1312906733.746 0.0 Angles 142.695358 23972.820 0.0 Propers102.167104 23396.267 0.0 Impropers 28.9844626028.768 0.0 RB-Dihedrals 2.885948 712.829 0.0 Pos. Restr. 38.1990441909.952 0.0 Virial3918.844696 70539.205 0.1 Settle2534.725856 818716.451 1.0 - Total78323890.379 100.0 - R E A L C Y C L E A N D T I M E A C C O U N T I N G Computing: Nodes Number G-CyclesSeconds % --- Neighbor search1 1136230337.457 6067.718.8 Force 1 1136235859.263 7172.122.3 PME mesh 1 1136212486.060 2497.3 7.8 Constraints1 22723 1294.000 258.8 0.8 Rest 1 81096.73016219.850.3 --- Total 1 161073.51132215.7 100.0 --- --- PME spread/gather 1 22724 7169.616 1434.0 4.5 PME 3D-FFT 1
