[gmx-users] error of equilibration

[s lal badshah]

Dear Justin & Mark,
Hi ! I am doing equilibration and again the error comes with the following warnings in the pr.log file,

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 224.227219 (between atoms 1932 and 1934) rms 4.182889
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    198    200   49.7    0.1449   0.1615      0.1449
    200    201   90.1    0.1090   1.2644      0.1090
    200    202   46.8    0.1529   0.1690      0.1529
    200    211   41.2    0.1522   0.1686      0.1522
................................ and so on
Then
Constraint error in algorithm Lincs at step 0
   Energies (kJ/mol)
          Angle    Proper Dih. Ryckaert-Bell.          LJ-14     Coulomb-14
    1.55786e+03    1.43449e+01    2.56063e+03    5.34585e+03    1.25360e+04
        LJ (SR)        LJ (LR)   Coulomb (SR)   Coul. recip. Position Rest.
    2.62155e+05   -1.69778e+03   -6.01840e+05   -1.97421e+21    1.12486e+00
      Potential    Kinetic En.   Total Energy    Temperature Pressure (bar)
   -1.97421e+21    4.12749e+07   -1.97421e+21    1.30857e+05   -4.47584e+17


Step 1  Warning: pressure scaling more than 1%, mu: -2.6855e+10 -2.6855e+10 -2.6855e+10

Step 1, time 0.002 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 10042.537109 (between atoms 1932 and 1933) rms 189.576416
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    170    172   63.5    0.1335   0.1514      0.1335
    172    173   41.5    0.1449   0.1421      0.1449
    172    181   87.7    0.1449   0.2690      0.1449
    173    174   38.6    0.1090   0.1403      0.1090
Then
Constraint error in algorithm Lincs at step 1
Correcting invalid box:
old box (3x3):
   old box[    0]={-1.94981e+11,  0.00000e+00, -0.00000e+00}
   old box[    1]={ 0.00000e+00, -1.94981e+11, -0.00000e+00}
   old box[    2]={ 0.00000e+00,  0.00000e+00, -1.94981e+11}
new box (3x3):
   new box[    0]={-1.94981e+11,  0.00000e+00, -0.00000e+00}
   new box[    1]={ 0.00000e+00, -1.94981e+11, -0.00000e+00}
   new box[    2]={ 0.00000e+00,  1.94981e+11, -1.94981e+11}
finaly
Fatal error:
Box was shifted at least 10 times. Please see log-file
Now will I start again from the begining by taking PDB file from RCSB ? or something else. I am checking the lincs warning page of gromacs but if you suggest me some correction it will be helpful.
Regards,
Lal badshah

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