[gmx-users] Help! LINCS WARNING &errors.

[SUN, Jian]

Dear all,

I am running simulated annealing for a protein in water and found something
strange:
1. the poteintial energy keep on rising while the system is cooling down
2. several LINCS WARNINGs are given (I have posted the question but no reply
till now) and then the energies become "nan"

Who can tell me why?

Thanks a lot.


the following is part of my logfile.

Constraint error in algorithm Lincs at step 263645


t = 263.645 ps: Water molecule starting at atom 70574 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with
previous and current coordinates
           Step           Time         Lambda
         263700      263.70001        0.00000


   Rel. Constraint Deviation:  Max    between atoms     RMS
       Before LINCS         0.000000      1      2   nan
        After LINCS         0.000000      1      2   nan


Current ref_t for group rest:    250.3
   Energies (kJ/mol)
          Angle    Proper Dih. Ryckaert-Bell.          LJ-14     Coulomb-14
            nan            nan            nan            nan            nan
        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.   Total Energy
    0.00000e+00    0.00000e+00            nan            nan            nan
    Temperature Pressure (bar)
            nan            nan


           Step           Time         Lambda
         263800      263.80002        0.00000


   Rel. Constraint Deviation:  Max    between atoms     RMS
       Before LINCS         0.000000      1      2   nan
        After LINCS         0.000000      1      2   nan
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