Jianhui Tian wrote:
Hi,
Thank you for the suggestions.
The water numbers should be fine. Becuase I can run the same system in
AMBER ok. I have done minimization. And the system explodes during the
equilibrium process.
I compared the energy of different component between AMBER and Gromacs.
For all these components, BOND energy always has big difference for the
same component between AMBER ang Gromacs. While the ANGLE, DIHEDRAL
and LJ etc are consistent with each other. I can't figure out why.
sounds like a periodic boundary problem. do you have molecules that are
broken over the PBC?
Try to fix that in that case. The mdrun version in CVS can handle it,
but not stock 3.3.1
Thanks.
Justin
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________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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