[gmx-users] Problem in energy minimization for a empty membrane system

[Mark Abraham]

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