[gmx-users] editconf and genbox using method

Marian Butu marian.butu at gmail.com
Mon Mar 9 11:23:50 CET 2009


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

Please, somebody help me with this problem.

PS. I'm a new user of Gromacs but I'm read all the messages from the
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.

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