[gmx-users] Questions about water in Gromacs

David van der Spoel spoel at xray.bmc.uu.se
Thu Aug 24 17:22:43 CEST 2006

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.
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://folding.bmc.uu.se

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