[gmx-users] Water molecule can not be settled

[Sunny]

Hi,

I have a structure with 1 protein (118 atoms), 256 DPPC lipids (12800 
atoms), and 3833 water molecules (11499 atoms). The box size is 6.125, 12.5, 
9.5 nm.

Water is add by genbox:    genbox -cp input.pdb -cs spc216.gro -vdwd 0.45 -o 
output.pdb

After the water added, I run the l-bfgs energy minimization on it.

Then I run md simulation (integrator=md, dt=0.002). The md simulation fails 
with a Segmentatin fault and the following message in md.log:

Step -2, time -0.001 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 9.488017 (between atoms 48 and 49) rms 0.158390
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
      1      5   30.2    0.0554   0.1507      0.1470
      6      7   32.2    0.1284   0.1220      0.1230
     ... ...
  12896  12897   60.6    0.4879   0.2176      0.1530
  12897  12898   55.7    0.2474   0.1692      0.1530
Constraint error in algorithm Lincs at step -2
Going to use C-settle (3833 waters)
wo = 0.888096, wh =0.0559521, wohh = 18.0154, rc = 0.08165, ra = 0.00646074
rb = 0.0512738, rc2 = 0.1633, rone = 1, dHH = 0.1633, dOH = 0.1

Constraining the coordinates at t0-dt (step -1)
   Rel. Constraint Deviation:  Max    between atoms     RMS
       Before LINCS         9.488017     48     49   0.158390
        After LINCS         50.828369     43     48   0.866281

Step -1, time -0.0005 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 50.828369 (between atoms 43 and 48) rms 0.866281
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
     33     35   39.5    0.1502   0.1805      0.1470
     35     36   40.8    0.1541   0.1945      0.1530
     ... ...
   5697   5698   69.7    0.1900   0.1719      0.1530
   6865   6866   93.4    0.1876   0.1722      0.1530
Constraint error in algorithm Lincs at step -1
Started mdrun on node 0 Wed Jan 17 13:50:30 2007
Initial temperature: 7.0078e+06 K
           Step           Time         Lambda
              0        0.00000        0.00000

Grid: 12 x 25 x 19 cells
Configuring nonbonded kernels...

There are 24417 atoms in your xtc output selection
   Rel. Constraint Deviation:  Max    between atoms     RMS
       Before LINCS         40346476102025216.000000   1367   1368   
507031760928768.000000
        After LINCS         39707178809950208.000000   1367   1368   
484342119792640.000000

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 39707178809950208.000000 (between atoms 1367 and 1368) rms 
484342119792640.000000
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
      1      2   91.8    0.0966 4259.4292      0.1000
      1      3  113.4    0.0993 4259.4448      0.1000
      ... ...
  12897  12898   89.4    0.1692 5628.2495      0.1530
  12898  12899   91.9    0.1592 438.1604      0.1530
Constraint error in algorithm Lincs at step 0

t = 0.000 ps: Water molecule starting at atom 15877 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): -50006056.00000, 291892.96875, 10607907.00000, 
ekin-cm:  3.37458e+20
   Energies (kJ/mol)
          Angle       G96Angle    Proper Dih. Ryckaert-Bell.  Improper Dih.
    9.54095e+04    1.09247e+04    1.06727e+04    2.10367e+04    5.80276e+03
          LJ-14     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.
    1.50514e+04    2.85987e+04    2.60953e+20   -1.27608e+05   -2.07571e+05
      Potential    Kinetic En.   Total Energy    Temperature Pressure (bar)
    2.60953e+20            INF            INF            INF            INF

How can I fix this error?

Thanks,

Sunny

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