[gmx-users] vacum simulation

[Souilem Safa]

Dear Gromacs users ,
 I did the simulation of a single molecule in vacum. I have choosed 10 ns
which corresponds to 5000000 steps. I was checking the .log file frequently.
I have noticed that the number of steps from 1938900 didn't increases.
When I open a new tab with the top option, I see mdrun still existing.
I have attached here the .log file and also some warnings that I saw when
steps stop at 1938900

Step 1938969, time 3877.94 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 12871303501.643789, max 33207281664.000000 (between atoms 3 and 6)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
     46     47   98.8    0.1406 3889.8669      0.1000
     45     46   79.4  10193.8799 10564.2393      0.1440
     43     44   79.6    0.1033 631.2256      0.1000
     42     45   80.1  10193.9062 11014.6123      0.1520
     42     43   93.5    0.1851 4970.4243      0.1440
     40     41   76.5    0.1009 184.9659      0.1000
     39     42   90.4    0.1819 5231.5186      0.1520
     39     40  100.0    0.1502 624.0559      0.1440
     37     38   97.1    0.1001 592.4050      0.1000
     36     37   81.4    0.1469 828.7896      0.1430
     35     39   88.6    0.1742 8071.4395      0.1520
     35     36   94.7    0.1861 8093.3452      0.1530
     35     34   92.9  8046.3804 17904.5762      0.1440
     33     45   78.0  26093.2402 332765.5000      0.1520
     33     34   94.6  26065.5371 330302.5625      0.1440
     29     30   74.4  190965.5938 1213272.0000      0.1360
     27     28   91.2  85465.0547 294693.5000      0.1430
     25     27   85.7  126649.9141 1143663.7500      0.1360
     25     26  107.7  116051.3750 805165.8125      0.1230
     24     29  102.8  1939418.3750 1702562.5000      0.1390
     24     25  101.0  1963544.3750 1402288.3750      0.1390
     22     23   97.9  345568.0625 1364901.0000      0.1530
     31     21  109.7  1948370.1250 7003795.5000      0.1390
     21     22  101.2  2108572.2500 6662917.5000      0.1390
     20     24   89.4  8876732.0000 68351760.0000      0.1390
     20     21   89.1  8780558.0000 67941296.0000      0.1390
     20     19   88.5  39924512.0000 280068256.0000      0.1530
     17     19   92.9  371385600.0000 509824768.0000      0.1530
     17     18   96.4  394707616.0000 358144416.0000      0.1230
     17     16   90.0  446916736.0000 883243840.0000      0.1360
     15     16   98.9  1051905920.0000 370290400.0000      0.1430
     14     15  100.8  520221760.0000 522257472.0000      0.1530
     13     14  128.2  1139173888.0000 3275473920.0000      0.1390
     13     11  155.0  2786396928.0000 3396753920.0000      0.1390
     11     12  151.7  1220930176.0000 2911329792.0000      0.1090
      9     11  161.5  369404096.0000 3428640000.0000      0.1390
      9     10  135.8  2190610944.0000 1502276608.0000      0.1090
      7      8   91.7  148944928.0000 1389486464.0000      0.1000
      6      9  150.6  497182528.0000 4613532672.0000      0.1390
      6      7  168.3  1652069120.0000 3562507776.0000      0.1360
      4      5  165.5  55138408.0000 449667456.0000      0.1000
      3      6  169.0  1702803200.0000 4615812096.0000      0.1390
      3      4  124.7  198457328.0000 2500093184.0000      0.1360
     13      1  158.1  1042088320.0000 3730094848.0000      0.1390
Wrote pdb files with previous and current coordinates
Please I need your help what should I do in this case?
Best regards,
Safa