[gmx-users] center peptide in simulation box

Mark Abraham Mark.Abraham at anu.edu.au
Wed Nov 3 22:53:17 CET 2010

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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