[gmx-users] step.pdb files with titel "one step before crash"

Tue May 30 17:42:27 CEST 2006

Dear all,

I am trying to run mdrun. It always prompts the following message and 
creates two pdb files stepN.pdb and #stepN.pdb.1# (where N is the step 
number) in each step. A stepN.pdb has a TITLE line "one step before crash" 
and #stepN-1.pdb.1 has a TITLE "crash". I'd like to know what's wrong in the 
run.

The message given in each step is like:

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.003179 (between atoms 41 and 42) rms 0.000636
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
      8      9   32.0    0.1000   0.1001      0.1000
     41     42   32.0    0.1000   0.1003      0.1000
     81     82   31.1    0.1000   0.1002      0.1000
     86     87   34.1    0.1000   0.1002      0.1000
    103    104   33.1    0.1000   0.1000      0.1000
    112    113   52.4    0.1000   0.1002      0.1000

step 0
Step 1, time 0.01 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 1.791684 (between atoms 112 and 113) rms 0.392409
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
      1      2   84.9    0.1000   0.1038      0.1000
      1      3   89.9    0.1000   0.1257      0.1000
      1      4   89.9    0.1000   0.1432      0.1000
      8      9   89.8    0.1001   0.2546      0.1000
     16     17   89.8    0.1001   0.1032      0.1000
     25     26   62.7    0.1090   0.1090      0.1090
     27     28   53.6    0.1090   0.1090      0.1090
     33     34   46.9    0.1000   0.1002      0.1000
     41     42   89.8    0.1003   0.2351      0.1000
     50     51   89.9    0.1000   0.2237      0.1000
     55     56   89.9    0.1000   0.1733      0.1000
     60     61   43.5    0.1090   0.1088      0.1090
     68     69   89.9    0.1090   0.1182      0.1090
     72     73   89.8    0.0999   0.1973      0.1000
     81     82   89.8    0.1002   0.2485      0.1000
     86     87   89.9    0.1002   0.2528      0.1000
     91     92   89.8    0.1090   0.1135      0.1090
     93     94   50.0    0.1090   0.1094      0.1090
     95     96   89.9    0.1090   0.1674      0.1090
     99    100   89.9    0.1090   0.1629      0.1090
    103    104   89.8    0.1000   0.2644      0.1000
    112    113   89.9    0.1002   0.2792      0.1000
Wrote pdb files with previous and current coordinates

Step 2, time 0.02 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 4.853224 (between atoms 1 and 2) rms 0.722267
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
      1      2   90.0    0.1038   0.5853      0.1000
      1      3   90.0    0.1257   0.4489      0.1000
      1      4   90.0    0.1432   0.4522      0.1000
      8      9   90.3    0.2546   0.1630      0.1000
     16     17   90.2    0.1032   0.1728      0.1000
     21     22   51.4    0.1091   0.1112      0.1090
     23     24   34.8    0.1093   0.1092      0.1090
     25     26   90.0    0.1090   0.2750      0.1090
     27     28   89.9    0.1090   0.2709      0.1090
     29     30   72.0    0.1092   0.1090      0.1090
     33     34   89.9    0.1002   0.2651      0.1000
     41     42   35.6    0.2351   0.1006      0.1000
     50     51   45.3    0.2237   0.1008      0.1000
     55     56   35.2    0.1733   0.1004      0.1000
     60     61   89.8    0.1088   0.2472      0.1090
     62     63   32.4    0.1092   0.1099      0.1090
     64     65   90.0    0.1086   0.2254      0.1090
     68     69   90.0    0.1182   0.1829      0.1090
     72     73   37.4    0.1973   0.1009      0.1000
     81     82   34.7    0.2485   0.1007      0.1000
     91     92   90.2    0.1135   0.2354      0.1090
     93     94   90.0    0.1094   0.2507      0.1090
     95     96   90.2    0.1674   0.1282      0.1090
     99    100   89.6    0.1629   0.1165      0.1090
    103    104   90.9    0.2644   0.1102      0.1000
    112    113   41.3    0.2792   0.1012      0.1000

Back Off! I just backed up step1.pdb to ./#step1.pdb.1#
Wrote pdb files with previous and current coordinates

Step 3, time 0.03 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 4.451822 (between atoms 60 and 61) rms 0.614110
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
     21     22   89.9    0.1112   0.2640      0.1090
     23     24   90.0    0.1092   0.1886      0.1090
     25     26   35.7    0.2750   0.1124      0.1090
     27     28   33.7    0.2709   0.1111      0.1090
     29     30   89.9    0.1090   0.2706      0.1090
     33     34   36.4    0.2651   0.1005      0.1000
     41     42   90.0    0.1006   0.2461      0.1000
     50     51   90.0    0.1008   0.2485      0.1000
     55     56   89.9    0.1004   0.2663      0.1000
     60     61   89.8    0.2472   0.5942      0.1090
     62     63   89.7    0.1099   0.1401      0.1090
     64     65   52.8    0.2254   0.1161      0.1090
     66     67   89.7    0.1096   0.1386      0.1090
     72     73   90.0    0.1009   0.2522      0.1000
     81     82   90.0    0.1007   0.2819      0.1000
     86     87   89.9    0.1003   0.3104      0.1000
     93     94   90.1    0.2507   0.1387      0.1090
     97     98   89.6    0.1081   0.1885      0.1090
    103    104   90.0    0.1102   0.1296      0.1000
    112    113   90.0    0.1012   0.2632      0.1000

Back Off! I just backed up step2.pdb to ./#step2.pdb.1#
Wrote pdb files with previous and current coordinates
.... ...

Thanks,

George

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