[gmx-users] (no subject)

[Sunil Thapa]

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
and 
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
Neal 


      
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