<div dir="ltr"><div>Hi gmx-users,</div>
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<div>My system has a 7*7*22 box and 3dc geometry for PME is applid (large vacuum space is in the z direction. I found a crash caused by particles communicated to PME node. Note that this problem had a fix already (<a href="http://www.gromacs.org/component/option,com_wrapper/Itemid,90/">http://www.gromacs.org/component/option,com_wrapper/Itemid,90/</a>), I was afraid that it would not be fixed in PME3DC, because this problem did not occur when I shift to geometry=3d. Both 4.0rc1 and the latest CVS version had this error. Thanks for your suggestions.</div>
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<div>-----------------------------------------------------output-------------------------------------------------------------------------<br>Step 695, time 1.39 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>
rms 0.000001, max 0.000003 (between atoms 4610 and 4616)<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br> 4570 4576 30.6 0.1000 0.1000 0.1000</div>
<p>Step 696, time 1.392 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>rms 0.000001, max 0.000004 (between atoms 4486 and 4492)<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br>
4570 4576 34.3 0.1000 0.1000 0.1000</p>
<p>Step 697, time 1.394 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>rms 0.000002, max 0.000011 (between atoms 464 and 470)<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length</p>
<p>Step 697, time 1.394 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>rms 0.000001, max 0.000004 (between atoms 6586 and 6592)</p>
<p>Step 697, time 1.394 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>rms 0.000001, max 0.000003 (between atoms 3794 and 3800)<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length</p>
<p>Step 697, time 1.394 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>rms 0.000001, max 0.000004 (between atoms 5850 and 5856)<br> 6038 6044 47.9 0.1000 0.1000 0.1000<br>bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br> 4728 4734 30.9 0.1000 0.1000 0.1000<br> 904 910 58.9 0.1000 0.1000 0.1000<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length</p>
<p>Step 697, time 1.394 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>rms 0.248747, max 2.690606 (between atoms 3676 and 3682)<br> 4570 4576 30.1 0.1000 0.1000 0.1000<br>bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br> 3676 3682 90.0 0.1000 0.3691 0.1000<br>Wrote pdb files with previous and current coordinates</p>
<p>-------------------------------------------------------<br>Program mdrun, VERSION 4.0_rc1<br>Source code file: pme.c, line: 518</p>
<p>Fatal error:<br>2 particles communicated to PME node 2 are more than a cell length out of the domain decomposition cell of their charge group<br>-------------------------------------------------------</p>
<p>"Wicky-wicky Wa-wild West" (Will Smith)</p>
<p>Error on node 2, will try to stop all the nodes<br>Halting parallel program mdrun on CPU 2 out of 8</p>
<p>gcq#263: "Wicky-wicky Wa-wild West" (Will Smith)</p>
<p>-----------------------------------------------------------------------------<br>One of the processes started by mpirun has exited with a nonzero exit<br>code. This typically indicates that the process finished in error.<br>
If your process did not finish in error, be sure to include a "return<br>0" or "exit(0)" in your C code before exiting the application.</p>
<p>PID 15418 failed on node n0 (<a href="http://127.0.0.1">127.0.0.1</a>) with exit status 1.<br>-----------------------------------------------------------------------------</p></div>