[gmx-users] Forces and derivatives

David spoel at xray.bmc.uu.se
Sat Apr 9 10:43:56 CEST 2005

On Fri, 2005-04-08 at 16:39 -0400, Ken Rotondi wrote:
> Hi all,
> I was wondering if there was an easy way to output the energies and 
> first derivatives for the 10 or 20 atoms with the largest energies? 
> I've looked through the manual, but did not  find a way. Also, is there 
> a way to determine if there are overlapping (sterically clashing) atoms 
> in a structure?
For the latter problem you can use gmxcheck, for the first you can write
out all the forces, but there is no determination of energy per atom in
the code.
> Ken
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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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