[gmx-users] solvation

Jamie Seyed jamie.seyed at gmail.com
Thu Aug 13 17:37:00 CEST 2009

Dear all,
I want to know how can I use genbox to fill inside of the pore as well as a
layer outside. From the "man genbox" page I try to use -shell with a
negative value (?) but it put waters far from the outside of the pore and I
think it does not care about the sign. It seems strange to me because when I
had 10 10 10 in the last line of my f.gro, by a shell 0.5 or 0.2, I got a
layer of few molecule around the pore, but when I change it to 1. 1. 1., the
water molecules generated far away. I appreciate if someone tell me (1) how
I can add water inside the pore and (2) why changing the box size will give
a opposite result. Please advise..Thanks in advance/Jamie
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