[gmx-users] Mix solvent

Erik Marklund erikm at xray.bmc.uu.se
Thu Apr 27 13:46:45 CEST 2006

On Thu, 2006-04-27 at 18:30 +1000, Mark Abraham wrote:
> >
> > In God We Trust
> > Hello GMX users
> > I want to use gromacs program to study a protein in a solvent of the
> > mixture
> > of  30% methanol and  70% water. Would you please tell me how can I make
> > gro
> > 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.
> Mark

How about using trjorder on the system before manually removing waters
down to 70%. In that way it's easy to delete the ones most distant from
the protein, leaving a continuous void in which methanol molecules are
more easily inserted. You will end up with a inhomogenous solvent for
sure, but it probably get mixed very quickly.

Erik Marklund, PhD student
Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.

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