editconf -f peptide.pdb/.gro -o peptide_center_in_simulation_box.gro -center x/2 y/2 z/2 -box x y z genbox -cp peptide_center_in_simulation_box.gro -cs spc216.gro -o they_are_in_the_same_box_now.gro -p topol.top
hth, lina ________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Mark Abraham [mark.abra...@anu.edu.au] Sent: Thursday, November 04, 2010 5:53 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] center peptide in simulation box On 3/11/2010 9:04 PM, leila karami wrote: Dear Mark Abraham In March 2010, In reply to question about [center peptide in simulation box], You answered: OK, well keep playing with the trjconv options and choosing sensible groups for centering until you find something that pleases you. You may need to do two different trjconv operations - one to center the peptide and one to group the waters in the same periodic cell as the peptide. I want to know how can I do last (group the waters in the same periodic cell as the peptide)? I'd find the answer to this by reading trjconv -h and experimenting :-) Mark
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