Hi Wang Zhun,<br>
<br>
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.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br><br><div><span class="gmail_quote">On 12/25/05, <b class="gmail_sendername">Wang Zhun</b> <<a href="mailto:wangzhun@pumc.edu.cn">wangzhun@pumc.edu.cn</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,all,Merry Christmas!<br><br>A question during solvating my extended peptide with different boxes:<br><br>editconf -f conf -o -d 0.5 -c -bt cubic<br>genbox -cp out -cs -o -p<br>produced a box of 745.73nm3 with 24741 water molecules
<br><br>editconf -f conf -o -d 0.5 -c<br>produced a box of 90.87nm3 with 3016 water molecules<br><br>editconf -f conf -o -d 0.5 -c -bt dodecahedron<br>produced a box of 527.31nm3 with 17394 water molecules<br><br>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.<br>And my peptide is solved completely in the first 2 boxes. Why this happened?<br><br><br>_______________________________________________<br>gmx-users mailing list<br><a href="mailto:gmx-users@gromacs.org">
gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to
<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br></blockquote></div><br><br clear="all"><br>-- <br><br>Tsjerk A. Wassenaar, M.Sc.<br>Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
<br>Dept. of Biophysical Chemistry<br>University of Groningen<br>Nijenborgh 4<br>9747AG Groningen, The Netherlands<br>+31 50 363 4336<br>