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<p class="MsoNormal" style="MARGIN: 0mm 0mm 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'"><font face="arial,helvetica,sans-serif">Hi,</font></span></p>
<p class="MsoNormal" style="MARGIN: 0mm 0mm 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'"><font face="arial,helvetica,sans-serif">I want to obtain a dodecahedron box to start a simulation of a small peptide. But, even if I use dodecahedron option or octahedron, I obtain a rectangular box.</font></span></p>
<p class="MsoNormal" style="MARGIN: 0mm 0mm 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'"><font face="arial,helvetica,sans-serif"> </font></span></p>
<p class="MsoNormal" style="MARGIN: 0mm 0mm 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'"><font face="arial,helvetica,sans-serif">Gromacs version: 4.0.4 compiled on redhat server 5 (I do this after 3.2.1 binaries for MS Windows)</font></span></p>
<p class="MsoNormal" style="MARGIN: 0mm 0mm 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'"><font face="arial,helvetica,sans-serif">Command line that I used:</font></span></p>
<p class="MsoNormal" style="MARGIN: 0mm 0mm 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'"><font face="arial,helvetica,sans-serif"> pdb2gmx -f pep1.pdb -p pep1.top -o pep1.gro -water tip3p</font></span></p>
<p class="MsoNormal" style="MARGIN: 0mm 0mm 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'"><font face="arial,helvetica,sans-serif"> editconf -f pep1 -o -bt octahedron -d 0.3 -c</font></span></p>
<p class="MsoNormal" style="MARGIN: 0mm 0mm 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'"><font face="arial,helvetica,sans-serif"> genbox -cp out -cs -p pep1 -o pep1_em</font></span></p>
<p class="MsoNormal" style="MARGIN: 0mm 0mm 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'"><font face="arial,helvetica,sans-serif"> </font></span></p>
<p class="MsoNormal" style="MARGIN: 0mm 0mm 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'"><font face="arial,helvetica,sans-serif">And, when I'm looking to pep1_em.gro with VMD the box is very very rectangular.</font></span></p>
<p class="MsoNormal" style="MARGIN: 0mm 0mm 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'"><font face="arial,helvetica,sans-serif"> </font></span></p>
<p class="MsoNormal" style="MARGIN: 0mm 0mm 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'"><font face="arial,helvetica,sans-serif">Please, somebody help me with this problem.</font></span></p>
<p class="MsoNormal" style="MARGIN: 0mm 0mm 0pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'"><font face="arial,helvetica,sans-serif"> </font></span></p>
<p class="MsoNormal" style="MARGIN: 0mm 0mm 6pt; LINE-HEIGHT: normal"><span style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman','serif'; mso-fareast-font-family: 'Times New Roman'"><font face="arial,helvetica,sans-serif">PS. I'm a new user of Gromacs but I'm read all the messages from the <span style="COLOR: green"><a href="http://www.mail-archive.com/gmx-users@gromacs.org"><span style="COLOR: blue">www.mail-archive.com/gmx-users@<b>gromacs</b>.org</span></a> </span>about this problem but I still don't understand what I need to do to obtain the correct box.</font></span></p>
<p class="MsoNormal" style="MARGIN: 0mm 0mm 10pt"><font face="arial,helvetica,sans-serif" size="3"> </font></p>
<p class="MsoNormal" style="MARGIN: 0mm 0mm 10pt"><font face="arial,helvetica,sans-serif" size="3">Thank you very much in advance for any suggestion.</font></p>
<p class="MsoNormal" style="MARGIN: 0mm 0mm 10pt"><font face="arial,helvetica,sans-serif" size="3">Marian</font></p></div>
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