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
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