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 <[email protected]>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 > 11357 11357.00000 0.00000 > > Step Time Lambda > 11358 11358.00000 0.00000 > > Step Time Lambda > 11359 11359.00000 0.00000 > > Step Time Lambda > 11360 11360.00000 0.00000 > > Step Time Lambda > 11361 11361.00000 0.00000 > > > 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=Tabulated W3=SPC/TIP3p W4=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] 141595.844211 54089612.489 69.1 > Outer nonbonded loop 18947.604080 189476.041 0.2 > 1,4 nonbonded interactions 105.189396 9467.046 0.0 > Calc Weights 11755.000218 423180.008 0.5 > Spread Q Bspline 250773.337984 501546.676 0.6 > Gather F Bspline 250773.337984 1504640.028 1.9 > 3D-FFT 1217431.505524 9739452.044 12.4 > Solve PME 14842.953216 949949.006 1.2 > NS-Pairs 418574.562328 8790065.809 11.2 > Reset In Box 1338.886718 4016.660 0.0 > Shift-X 3916.765450 23500.593 0.0 > CG-CoM 3918.333406 11755.000 0.0 > Bonds 114.131290 6733.746 0.0 > Angles 142.695358 23972.820 0.0 > Propers 102.167104 23396.267 0.0 > Impropers 28.984462 6028.768 0.0 > RB-Dihedrals 2.885948 712.829 0.0 > Pos. Restr. 38.199044 1909.952 0.0 > Virial 3918.844696 70539.205 0.1 > Settle 2534.725856 818716.451 1.0 > > ----------------------------------------------------------------------------- > Total 78323890.379 100.0 > > ----------------------------------------------------------------------------- > > > 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-Cycles Seconds % > ----------------------------------------------------------------------- > Neighbor search 1 11362 30337.457 6067.7 18.8 > Force 1 11362 35859.263 7172.1 22.3 > PME mesh 1 11362 12486.060 2497.3 7.8 > Constraints 1 22723 1294.000 258.8 0.8 > Rest 1 81096.730 16219.8 50.3 > ----------------------------------------------------------------------- > Total 1 161073.511 32215.7 100.0 > ----------------------------------------------------------------------- > ----------------------------------------------------------------------- > PME spread/gather 1 22724 7169.616 1434.0 4.5 > PME 3D-FFT 1 22724 3654.067 730.8 2.3 > PME solve 1 11362 1662.017 332.4 1.0 > ----------------------------------------------------------------------- > > NODE (s) Real (s) (%) > Time: 2137.029 32215.651 6.6 > 35:37 > (Mnbf/s) (GFlops) (steps/hour) > Performance: 609.130 78323.890 19140.2 > Finished mdrun on node 0 Sat Jan 1 02:54:31 2011 > > > hepl me ! > > > regards : > shikha > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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