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
simulation.
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.
________________________________________________________________________
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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