Re: [gmx-users] editconf/genbox: molecular complex outside simulation box

thanks. things are getting clearer and life's going a little easier, now. Justin A. Lemkul schrieb: dur...@zib.de wrote: hi there, it's my first steps with gromacs and i can't get rid of the following problem: i set up my box with editconf -bt dodecahedron -f complex.pdb -o

[gmx-users] editconf/genbox: molecular complex outside simulation box

hi there, it's my first steps with gromacs and i can't get rid of the following problem: i set up my box with editconf -bt dodecahedron -f complex.pdb -o complex.pdb -c -d 0.9 and fill it up with water like genbox -cp complex.pdb -cs ffamber_tip3p.gro -o outfile.pdb -p complex.top but when

Re: [gmx-users] editconf/genbox: molecular complex outside simulation box

dur...@zib.de wrote: hi there, it's my first steps with gromacs and i can't get rid of the following problem: i set up my box with editconf -bt dodecahedron -f complex.pdb -o complex.pdb -c -d 0.9 and fill it up with water like genbox -cp complex.pdb -cs ffamber_tip3p.gro -o outfile.pdb