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

[David van der Spoel]

SUN, Jian wrote:
> 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
conservation of energy?

> 2. several LINCS WARNINGs are given (I have posted the question but no 
> reply till now) and then the energies become "nan"
bad structures. check mailing list archives.

> 
> 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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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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