Dear all,<br>
<br>
I am running simulated annealing for a protein in water and found something strange:<br>
1. the poteintial energy keep on rising while the system is cooling down<br>
2. several LINCS WARNINGs are given (I have posted the question but no reply till now) and then the energies become "nan"<br>
<br>
Who can tell me why? <br>
<br>
Thanks a lot.<br>
<br>
<br>
the following is part of my logfile.<br>
<br>
Constraint error in algorithm Lincs at step 263645<br>
<br>
t = 263.645 ps: Water molecule starting at atom 70574 can not be settled.<br>
Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates<br>
Step
Time Lambda<br>
263700
263.70001 0.00000<br>
<br>
Rel. Constraint Deviation: Max between atoms RMS<br>
Before
LINCS
0.000000 1
2 nan<br>
After
LINCS
0.000000 1
2 nan<br>
<br>
Current ref_t for group rest: 250.3<br>
Energies (kJ/mol)<br>
Angle Proper Dih.
Ryckaert-Bell.
LJ-14 Coulomb-14<br>
nan
nan
nan
nan
nan<br>
LJ (SR) Coulomb
(SR) Potential Kinetic
En. Total Energy<br>
0.00000e+00
0.00000e+00
nan
nan
nan<br>
Temperature Pressure (bar)<br>
nan
nan<br>
<br>
Step
Time Lambda<br>
263800
263.80002 0.00000<br>
<br>
Rel. Constraint Deviation: Max between atoms RMS<br>
Before
LINCS
0.000000 1
2 nan<br>
After
LINCS
0.000000 1
2 nan<br>
<br>