[gmx-users] editconf question

Tsjerk Wassenaar tsjerkw at gmail.com
Sun Dec 25 10:10:08 CET 2005

Hi Wang Zhun,

Merry Christmas to you too. What you're observing is due to the
representation of the rhombic dodecahedron as its corresponding rectangular
unit cell. This is not a problem. In the simulation you're unit cell will be
'stacked to infinity' and your peptide will be fully solvated. If you look
closely, you'll see that on the opposite side of where your peptide is
sticking out, there's a hole where that part will fit.



On 12/25/05, Wang Zhun <wangzhun at pumc.edu.cn> wrote:
> 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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Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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