[gmx-users] Protein out of water box

Adriana Pietropaolo adriana at ms.fci.unibo.it
Wed Mar 15 14:34:13 CET 2006

On Wed, 15 Mar 2006, Prasad Gajula wrote:

> Dear Gromacs Users,
> When I use the genbox after editconf , most of the protein is out of water.
> Even with 'trjconv' after the simulations I cant see any change, as
> suggested by other gromacs users.
> Pls some one give me an idea...
> thank you very much!
> best regards
> Gajula

Hi Gaiula,
when you generated your box did you use the option -center in editconf?
maybe an input box problem
if this, you have to use -center XYZ, where XYZ are half of the box 
good luck!
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Adriana Pietropaolo,
PhD student,
dipartimento di Chimica Fisica ed Inorganica,
Facolta' di Chimica Industriale
Universita' di Bologna
Tel 051/6446992
FAX 051/2093690 

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