[gmx-users] editconf question

Wang Zhun wangzhun at pumc.edu.cn
Sun Dec 25 04:50:26 CET 2005

Hi,all,Merry Christmas! 

A question during solvating my extended peptide with different boxes:

editconf -f conf -o -d 0.5 -c -bt cubic
genbox -cp out -cs -o -p   
produced a box of 745.73nm3 with 24741 water molecules

editconf -f conf -o -d 0.5 -c
produced a box of 90.87nm3 with 3016 water molecules

editconf -f conf -o -d 0.5 -c -bt dodecahedron
produced a box of 527.31nm3 with 17394 water molecules

As posted before, dodecahedron box is only 71% of a cubic box, but the strange thing is there is part of peptide out of the water box visualized by VMD.
And my peptide is solved completely in the first 2 boxes. Why this happened?

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