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gmembed_error.txt

Ozge Yoluk, 12/09/2014 01:32 PM

 
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step 500, remaining wall clock time:   144 s          
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step 531: Water molecule starting at atom 216133 can not be settled.
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Check for bad contacts and/or reduce the timestep if appropriate.
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Wrote pdb files with previous and current coordinates
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step 532: Water molecule starting at atom 216133 can not be settled.
7
Check for bad contacts and/or reduce the timestep if appropriate.
8
Wrote pdb files with previous and current coordinates
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step 533: Water molecule starting at atom 215506 can not be settled.
11
Check for bad contacts and/or reduce the timestep if appropriate.
12
Wrote pdb files with previous and current coordinates
13

    
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step 534: Water molecule starting at atom 216133 can not be settled.
15
Check for bad contacts and/or reduce the timestep if appropriate.
16
Wrote pdb files with previous and current coordinates
17

    
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step 535: Water molecule starting at atom 215506 can not be settled.
19
Check for bad contacts and/or reduce the timestep if appropriate.
20
Wrote pdb files with previous and current coordinates
21

    
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step 536: Water molecule starting at atom 216133 can not be settled.
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Check for bad contacts and/or reduce the timestep if appropriate.
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Wrote pdb files with previous and current coordinates
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./prep_commands.sh: line 118: 55024 Segmentation fault: 11  mdrun -nt 1 -s membed.tpr -membed membed.dat -c $NAME\_$MEMBRANE\_SOL.pdb -v