[gmx-users] Fmax consistently on same atom
spoel at xray.bmc.uu.se
Wed Jul 27 21:43:15 CEST 2005
On Wed, 2005-07-27 at 20:12 +0100, Joanne Hanna wrote:
> Can someone tell me if it is bad, or what the implications are of the
> highest value of Fmax in an em or md being consistently on the same
> atom, in my case the N of the NH2 of AMP. The structure looks okay as
> does the potential energy i think:
> Potential Energy = -3.4637453e+04
> Maximum force = 1.2780455e+03 on atom 5259
> Norm of force = 2.9982839e+03
> Any feedback is greatly appreciated.
this force is not extreme for a dynamics run. By the way maybe you have
to add one to the number and it is a H in a H-Bond.
What counts is not the force on an atom but on a group (i.e. the NH2
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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://xray.bmc.uu.se/~spoel
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