[gmx-users] minimization problems

David van der Spoel spoel at xray.bmc.uu.se
Thu Jan 8 10:46:56 CET 2009

Hongyan Xiao wrote:
> Hi, gmx-users,
> I built a system,decane(42molecule)/water(903)/decane(42), including the 
> two decane/water interfaces. However, when I minimized this system, I 
> found the system turn into  water/decane(84)/water. That is to say in 
> the initial system two parts of decane turn into a part, while water 
> turns into two parts. I am surprised by the minimized result. Can you 
> tell me the possible reasons? Thank you very much!

Periodic boundary conditions?
> H. Y. Xiao 
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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