Hi, 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.
Gromacs version: 4.0.4 compiled on redhat server 5 (I do this after 3.2.1 binaries for MS Windows) Command line that I used: pdb2gmx -f pep1.pdb -p pep1.top -o pep1.gro -water tip3p editconf -f pep1 -o -bt octahedron -d 0.3 -c genbox -cp out -cs -p pep1 -o pep1_em And, when I'm looking to pep1_em.gro with VMD the box is very very rectangular. Please, somebody help me with this problem. PS. I'm a new user of Gromacs but I'm read all the messages from the www.mail-archive.com/gmx-us...@*gromacs*.org<http://www.mail-archive.com/gmx-users@gromacs.org> about this problem but I still don't understand what I need to do to obtain the correct box. Thank you very much in advance for any suggestion. Marian
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