[gmx-users] Exploding molecules

David van der Spoel spoel at xray.bmc.uu.se
Wed Aug 31 07:02:22 CEST 2005

On Wed, 2005-08-31 at 06:55 +0800, Jeffrey Chua wrote:
> dear friends,
> sorry, im resending this again...
> we are trying to do an md simulation of 1,2-cyclohexanediol (in water)
> using OPLSAA as forcefield but the runs always end up with a
> segmentation fault error.  and when the trr files are converted and
> viewed using VMD, the molecule seems to have exploded, with the
> oxygens in the alcohol groups joining, and the whole molecule looks
> totally deformed.  could it be because of electrostatics? can anyone
> suggest a way on how to go about this (without calculating for
> electrostatic potentials anymore if it is because of the
> electrostatics).
probably a topology probably the topology. Check the exclusions, you may
need more
> thanks
> jeffchua
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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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