[gmx-users] center peptide in simulation box

leila karami karami.leila1 at gmail.com
Wed Nov 3 11:04:57 CET 2010

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
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

I want to know how can I do last (group the waters in the same
periodic cell as the peptide)?


Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
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