[gmx-users] Gromacs and system building

Matteus Lindgren matteus.lindgren at chem.umu.se
Tue Jul 22 13:41:27 CEST 2008

Hi all!


I am new to Gromacs and currently facing some beginners problems. I want to
create a urea and water solvent box, add protein and cut the cubic box into
a dodecahedron. 

I have been looking in the manual for gromacs programs that can do some
system building but cant really find what I want in genbox and genconf and
the others. 


If I want to translate a protein within a box, the protein has to be a
separate file and then translate it with editconf? No coordinate
manipulation for just one residue? 

How can I concatenate two coordinate files, .gro or .pdb, and how can I
renumber the residues when doing this? 

How can I remove all solvent outside of the dodecahedron from a cubic box?
In general, does gromacs have any molecule selection commands to use for
example to delete some molecules close to a certain residue or so?


I am used to Charmm and when using constant pressure algorithms the
trajectory shows the fluctuating volume of the box. Have those fluctuations
been removed in Gromacs trajectories? 


Thank you



Matteus Lindgren 

Graduate student 


Department of Chemistry
Umeå University
SE-901 87 Umeå, Sweden
Tel: +46 (0)90 786 53 68
e-mail:  <mailto:barbara.addario at chem.umu.se> matteus.lindgren at chem.umu.se


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