[gmx-users] problems with energy minimization
David van der Spoel
spoel at xray.bmc.uu.se
Mon Aug 28 14:46:40 CEST 2006
> 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,
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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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