<P>Hello everyone<BR itxtvisited="1">I am doing MD on a protein, and everything including the EM seems to go well. When I start to do the position restrained MD (or even directly the MD without doing the PR MD), I get a "Segmentation fault". </P>
<P>when a doing EM,I set nsteps = 500,because i just want to go though the procedures,but there is a result:</P>
<P>Steepest Descents did not converge to Fmax < 1000 in 501 steps.</P>
<P> i go on the grompp pr.mdp and mdrun command, Segmentation fault comes up.details as followed:</P>
<P>Step -2, time -0.004 (ps) LINCS WARNING<BR>relative constraint deviation after LINCS:<BR>max 0.060225 (between atoms 4110 and 4112) rms 0.001990<BR>bonds that rotated more than 30 degrees:<BR> atom 1 atom 2 angle previous, current, constraint length<BR>starting mdrun 'CYP2W1_CYSHEME in water'<BR>100 steps, 0.2 ps.</P>
<P><BR>Step 0, time 0 (ps) LINCS WARNING<BR>relative constraint deviation after LINCS:<BR>max 20.941092 (between atoms 4012 and 4013) rms 0.630786<BR>bonds that rotated more than 30 degrees:<BR> atom 1 atom 2 angle previous, current, constraint length<BR> 4008 4010 59.8 0.1470 0.2246 0.1470<BR> 4010 4011 87.3 0.1536 1.1098 0.1530<BR> 4010 4023 56.2 0.1530 0.2198 0.1530</P>
<P>........</P>
<P>........ so much atoms number<BR> Warning: 1-4 interaction between 4008 and 4012 at distance 1.404 which is larger than the 1-4 table size 1.000 nm<BR>These are ignored for the rest of the simulation<BR>This usually means your system is exploding,<BR>if not, you should increase table-extension in your mdp file</P>
<P>Step 1, time 0.002 (ps) LINCS WARNING<BR>relative constraint deviation after LINCS:<BR>max 10879059641262569160704.000000 (between atoms 4029 and 4030) rms 157073328433382031360.000000<BR>bonds that rotated more than 30 degrees:</P>
<P> atom 1 atom 2 angle previous, current, constraint length<BR> 933 935 38.7 0.1330 0.1811 0.1330<BR> 935 936 41.3 0.1000 0.1411 0.1000</P>
<P>................so much atoms number</P>
<P> 4210 4212 52.3 0.1330 0.2032 0.1330<BR> 4212 4213 30.8 0.1000 0.1209 0.1000</P>
<P>Wrote pdb files with previous and current coordinates<BR>[localhost:09678] *** Process received signal ***<BR>[localhost:09678] Signal: Segmentation fault (11)<BR>[localhost:09678] Signal code: Address not mapped (1)<BR>[localhost:09678] Failing at address: 0x5ad01b00<BR>[localhost:09678] [ 0] /lib/tls/libpthread.so.0 [0xab68b0]<BR>[localhost:09678] [ 1] mdrun(do_nonbonded+0x349) [0x816d4a1]<BR>[localhost:09678] *** End of error message ***<BR>Segmentation fault<BR></P>
<P><EM> </EM>I have been trying to solve this problem for quite some time now. It would be very helpful if you can suggest some way to work around this problem.<BR>thanks!</P>
<P>jianlu guo</P><br><br><span title="neteasefooter"/><hr/>
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