hi,<br>HAPPY NEW YEAR<br><br>I am experiencing a segmentation fault during mdrun in equlibration step . <br>error <br><br>Wrote pdb files with previous and current coordinates<br>[shikha-desktop:01719] *** Process received signal ***<br>
[shikha-desktop:01719] Signal: Segmentation fault (11)<br>[shikha-desktop:01719] Signal code: Address not mapped (1)<br>[shikha-desktop:01719] Failing at address: 0x8d22a70<br>[shikha-desktop:01719] [ 0] [0xb87410]<br>[shikha-desktop:01719] [ 1] mdrun(do_nonbonded+0x769) [0x82a9789]<br>
[shikha-desktop:01719] *** End of error message ***<br>Segmentation fault<br><br><br><br><br><br>bottom lines of my .log file after energy minimization is this <br><br><br><br> Step Time Lambda<br> 11357 11357.00000 0.00000<br>
<br> Step Time Lambda<br> 11358 11358.00000 0.00000<br><br> Step Time Lambda<br> 11359 11359.00000 0.00000<br><br> Step Time Lambda<br>
11360 11360.00000 0.00000<br><br> Step Time Lambda<br> 11361 11361.00000 0.00000<br><br><br>Stepsize too small, or no change in energy.<br>Converged to machine precision,<br>
but not to the requested precision Fmax < 1000<br><br>Double precision normally gives you higher accuracy.<br>You might need to increase your constraint accuracy, or turn<br>off constraints alltogether (set constraints = none in mdp file)<br>
<br>Steepest Descents converged to machine precision in 11362 steps,<br>but did not reach the requested Fmax < 1000.<br>Potential Energy = -5.4871900e+06<br>Maximum force = 3.9830833e+03 on atom 4511<br>Norm of force = 1.9521437e+01<br>
<br> M E G A - F L O P S A C C O U N T I N G<br><br> RF=Reaction-Field FE=Free Energy SCFE=Soft-Core/Free Energy<br> T=Tabulated W3=SPC/TIP3p W4=TIP4p (single or pairs)<br> NF=No Forces<br><br> Computing: M-Number M-Flops % Flops<br>
-----------------------------------------------------------------------------<br> LJ 10523.695513 347281.952 0.4<br> Coul(T) 6405.625131 269036.256 0.3<br>
Coul(T) [W3] 226.446553 28305.819 0.0<br> Coul(T) + LJ 4637.739866 255075.693 0.3<br> Coul(T) + LJ [W3] 1706.661036 235519.223 0.3<br>
Coul(T) + LJ [W3-W3] 141595.844211 54089612.489 69.1<br> Outer nonbonded loop 18947.604080 189476.041 0.2<br> 1,4 nonbonded interactions 105.189396 9467.046 0.0<br>
Calc Weights 11755.000218 423180.008 0.5<br> Spread Q Bspline 250773.337984 501546.676 0.6<br> Gather F Bspline 250773.337984 1504640.028 1.9<br>
3D-FFT 1217431.505524 9739452.044 12.4<br> Solve PME 14842.953216 949949.006 1.2<br> NS-Pairs 418574.562328 8790065.809 11.2<br>
Reset In Box 1338.886718 4016.660 0.0<br> Shift-X 3916.765450 23500.593 0.0<br> CG-CoM 3918.333406 11755.000 0.0<br>
Bonds 114.131290 6733.746 0.0<br> Angles 142.695358 23972.820 0.0<br> Propers 102.167104 23396.267 0.0<br>
Impropers 28.984462 6028.768 0.0<br> RB-Dihedrals 2.885948 712.829 0.0<br> Pos. Restr. 38.199044 1909.952 0.0<br>
Virial 3918.844696 70539.205 0.1<br> Settle 2534.725856 818716.451 1.0<br>-----------------------------------------------------------------------------<br>
Total 78323890.379 100.0<br>-----------------------------------------------------------------------------<br><br><br> 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<br>
<br> Computing: Nodes Number G-Cycles Seconds %<br>-----------------------------------------------------------------------<br> Neighbor search 1 11362 30337.457 6067.7 18.8<br>
Force 1 11362 35859.263 7172.1 22.3<br> PME mesh 1 11362 12486.060 2497.3 7.8<br> Constraints 1 22723 1294.000 258.8 0.8<br> Rest 1 81096.730 16219.8 50.3<br>
-----------------------------------------------------------------------<br> Total 1 161073.511 32215.7 100.0<br>-----------------------------------------------------------------------<br>
-----------------------------------------------------------------------<br> PME spread/gather 1 22724 7169.616 1434.0 4.5<br> PME 3D-FFT 1 22724 3654.067 730.8 2.3<br> PME solve 1 11362 1662.017 332.4 1.0<br>
-----------------------------------------------------------------------<br><br> NODE (s) Real (s) (%)<br> Time: 2137.029 32215.651 6.6<br> 35:37<br> (Mnbf/s) (GFlops) (steps/hour)<br>
Performance: 609.130 78323.890 19140.2<br>Finished mdrun on node 0 Sat Jan 1 02:54:31 2011<br><br><br>hepl me !<br><br><br>regards :<br>shikha <br>