[gmx-users] (no subject)

Sunil Thapa mephysik at yahoo.com
Sun Oct 5 14:29:22 CEST 2008

hello gmx users
I am a new fellow in gromacs
My structure contains 56 residues belonging to parallel helices separated by about 2 nm.
I used editconf as:
editconf----- -bt dodecahedron -c
editconf---- -bt dodecahedron -d 6.5 -c 
where 6.5nm I used as separation of unit cells
Now when I solvated using spc216. In the first case, the number of solvent molecules was more than 117000 and in the second case it was 704. Moreover, in both the cases large number of atoms lied outside the box.
Can you tell me how to know the appropriate size of box for a protein structure like mine
Thanks in advance

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