[gmx-users] Gromacs and system building
matteus.lindgren at chem.umu.se
Tue Jul 22 13:41:27 CEST 2008
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
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
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?
Department of Chemistry
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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