[gmx-users] center peptide in simulation box

#ZHAO LINA# ZHAO0139 at e.ntu.edu.sg
Thu Nov 4 03:21:21 CET 2010

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


From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Mark Abraham [Mark.Abraham at 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 :-)

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