[gmx-users] problems with energy minimization

David van der Spoel spoel at xray.bmc.uu.se
Mon Aug 28 14:46:40 CEST 2006

Martin wrote:
> Dear all,
> I´m a beginner in the field of molecular dynamics and have just installed the 
> gromacs software.
> I have problems with energy minimization. When trying out the md tutorial on 
> the lysozyme structure 1AKI.pdb using the provided minim.mdp file the 
> minimization finishes with the message:

this is a FAQ, but the answer is, this result is fine as a start for MD 

>   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)
>   writing lowest energy coordinates.
>   Back Off! I just backed up minim_traj.trr to ./#minim_traj.trr.4#
>   Back Off! I just backed up confout.gro to ./#confout.gro.4#
>   Steepest Descents converged to machine precision in 79 steps,
>   but did not reach the requested Fmax < 1000.
>   Potential Energy  = -1.13948846313191e+04
>   Maximum force     =  1.94715000386709e+03 on atom 1113
>   Norm of force     =  8.53155624640669e+03
> I already tried different minimization algorithms with different settings and 
> also compiled the code with double precision accuracy without success.
> Thank you very much for any advice,
> Martin
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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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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