[gmx-users] Help!

Tsjerk Wassenaar t.a.wassenaar at chem.rug.nl
Tue Feb 17 16:08:01 CET 2004

Hi Ankur,

You don't need to decide on the number of water yourself, or know the 
size of your protein (which is easy enough to measure). What you do have 
to decide on is which box type you will use, the rest will follow.

The best choice is a rhombic dodecahedron, as it allows your protein to 
rotate freely. Or you can constrain rotational motions and do with a 
much smaller box, molecular shaped :p

For a rhombic dodecahedron use:

editconf -f 1qhk.gro -o 1qhk-rhbox -bt dodecahedron -d 1.0

Then to add solvent

genbox -cp 1qhk-rhbox.gro -cs -o 1qhk-sol

But that's all in the manual.



ankur gupta wrote:

>Dear Gromacs Users,
>I want to dissolve my protein 1qhk in water and then study the dynamics
>and structural properties of water-protein interface but I dont know how
>many water molecules should I take to dissolve the protein and also the
>size of the box.So please guide me how will we decide the no of water
>molecules and size of the box. Also I dont know the size of my protein so
>please tell me how to know the size of my protein.
>"You are making progress if each mistake You make is a new one"
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