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 Regards Matteus Lindgren Graduate student Department of Chemistry Umeå University SE-901 87 Umeå, Sweden Tel: +46 (0)90 786 53 68 e-mail: <mailto:[EMAIL PROTECTED]> [EMAIL PROTECTED]
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