Bing Bing wrote:
Hi! Thanks a alot for all the suggestions i've got from Justin and Mark.
I found out that i actually deleted the box information from the
starting structure PDB. Once i put it back, It worked. However,
it stopped with this message.
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)
That can be normal.
writing lowest energy coordinates.
Back Off! I just backed up em.trr to ./#em.trr.19#
Back Off! I just backed up em.gro to ./#em.gro.11#
Steepest Descents converged to machine precision in 76 steps,
but did not reach the requested Fmax < 1000.
Potential Energy = -2.24796600790506e+05
Maximum force = 1.14539522791599e+03 on atom 6619
Norm of force = 1.62353061702859e+04
Is it mean that the minimization is done and is already converged?
Here the result for the final Step 75.
Energies (kJ/mol)
Bond Angle Proper Dih. Ryckaert-Bell. Improper Dih.
1.23491e+03 9.85552e+03 4.48086e+03 4.81663e+03 1.33894e+03
LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip.
4.09985e+03 8.28955e+03 -1.68827e+04 -1.04035e+05 -1.38691e+05
Position Rest. Potential Kinetic En. Total Energy Temperature
6.95754e+02 -2.24797e+05 0.00000e+00 -2.24797e+05 0.00000e+00
Pressure (bar)
0.00000e+00
These all seem plausible. The proof is in MD running in a stable fashion.
Mark
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