[gmx-users] Mix solvent
mark.abraham at anu.edu.au
Thu Apr 27 10:30:38 CEST 2006
> In God We Trust
> Hello GMX users
> I want to use gromacs program to study a protein in a solvent of the
> of 30% methanol and 70% water. Would you please tell me how can I make
> file of "mix solvent" box for genbox.
There's no straightforward approach that I'm aware of. One possibility is
to do the arithmetic for the size box you want to use and generate a
smaller box filled with N water molecules that will give you 70% were you
to increase the size of the box and fill the gaps with methanol. Then
increase the size of the box, and use the -nmol and -ci options to genbox
to add enough methanols to make the mix 70/30. Then you will need to
equilibrate that box for a while to get a good mix of solvents at
reasonable density and pressure. I think you should be able to use that
box later for subsequently doing genbox for your protein.
You could also manually delete enough waters to get down to 70%, and use
the genbox options above to try to fill the gaps, but you will have a hard
time fitting methanol into water-sized holes.
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