[gmx-users] Problem in energy minimization for a empty membrane system
Mark.Abraham at anu.edu.au
Thu Jun 25 11:14:44 CEST 2009
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)
These all seem plausible. The proof is in MD running in a stable fashion.
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