[gmx-users] clashing happened inside the protein molecule?

[Chih-Ying Lin]

Hi
Here is my .out file.
atoms 366 and 368 are two atoms inside the protein.
What is other possible way to solve it ?


Thank you

Lin




relative constraint deviation after LINCS:
max 597108032.000000 (between atoms 366 and 368) rms 26394490.000000
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
     26     39   52.0    0.1530   0.1699      0.1530
     39     40   69.4    0.1230   0.1423      0.1230
     39     41   40.7    0.1330   0.1502      0.1330
     75     76   36.0    0.1250   0.1252      0.1250
    133    134   69.5    0.1530   0.1937      0.1530
    134    135   89.8    0.1470   0.2036      0.1470
    344    346   42.4    0.1470   0.2090      0.1470
    346    347   42.2    0.1530   0.2141      0.1530
    346    359   63.9    0.1530 26006.0332      0.1530
    359    360   56.9    0.1230 26006.0469      0.1230
    359    361   83.2    0.1330 82898.5859      0.1330
    361    362   77.5    0.1000 82845.7109      0.1000
    361    363   83.8    0.1470 398710.1875      0.1470
    363    364   89.3    0.1530 1909291.8750      0.1530
    363    369   85.2    0.1530 393002.8125      0.1530
    364    365   90.0    0.1508 31146174.0000      0.1530
    365    366   90.2    0.1544 66925512.0000      0.1530
    366    367   92.7    0.1301 73689816.0000      0.1250
    366    368   87.0    0.1305 74638504.0000      0.1250
    369    370   72.1    0.1230 65978.3203      0.1230
    369    371   72.6    0.1330 66864.2812      0.1330
    371    372   85.7    0.1000 10685.0596      0.1000
    371    373   61.0    0.1470 10685.1035      0.1470
    373    374   33.3    0.1530   0.1896      0.1530
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