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 &lt; 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 &lt; 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>