[gmx-users] position restrain problem

[Anthony Cruz]

Hi:
I am trying to run a position restrain dynamics of a protein that have 3 
parts. The energy minimization run for only 44 steps. When I try to run the 
position restrain I have the following error:

Step 6, time 0.012 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.011542 (between atoms 1462 and 1463) rms 0.000543
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
     62     63   32.3    0.0992   0.1000      0.1000
    305    306   35.2    0.0992   0.0998      0.1000
    354    355   30.3    0.1320   0.1330      0.1330
    381    382   31.2    0.0992   0.1000      0.1000
    580    581   40.9    0.0992   0.1000      0.1000
   1407   1409   30.2    0.0995   0.1003      0.1000
   1410   1412   54.3    0.0997   0.0992      0.1000
   1462   1463   79.8    0.0994   0.1012      0.1000
   1462   1464   43.7    0.0997   0.1007      0.1000
   1493   1495   32.2    0.0994   0.0997      0.1000
   1542   1543   31.4    0.0990   0.0996      0.1000
   1698   1699   34.5    0.0992   0.1000      0.1000
   1861   1863   35.3    0.0992   0.0997      0.1000
   1866   1867   30.1    0.0993   0.1000      0.1000
   2010   2012   30.0    0.0993   0.0997      0.1000

t = 0.012 ps: Water molecule starting at atom 3861 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with 
previous and current coordinates
Large VCM(group rest):     -0.00645,     -0.00647,      0.00685, ekin-cm:  
3.95311e+01

Step 7, time 0.014 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.013635 (between atoms 1462 and 1464) rms nan
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    305    306   34.5    0.0991   0.0999      0.1000
    669    670   33.5    0.1081   0.1089      0.1090
    862    863   48.7    0.0992   0.1002      0.1000
   1358   1359   37.3    0.0994   0.1004      0.1000
   1407   1409   31.8    0.0995   0.1001      0.1000
   1410   1412   34.1    0.0985   0.0995      0.1000
   1447   1448   34.6    0.1083   0.1093      0.1090
   1462   1463   71.5    0.1004   0.0993      0.1000
   1462   1464   30.6    0.0999   0.0986      0.1000
   1648   1649   44.7    0.1080   0.1086      0.1090
   1825   1826   30.0    0.1083   0.1092      0.1090
   1842   1843   36.3    0.0993   0.1001      0.1000
   1866   1867   30.7    0.0993   0.0999      0.1000
   2010   2011   44.7    0.0992   0.0999      0.1000
   2010   2012   37.2    0.0990   0.0992      0.1000

t = 0.014 ps: Water molecule starting at atom 3666 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with 
previous and current coordinates

How I can solve the problem???

Best regards

Anthony