[gmx-users] Re: Mix solvent
Jones de Andrade
johannesrs at gmail.com
Thu Apr 27 22:18:13 CEST 2006
Well, I don't know if the list allows the indication of "out-gromacs"
programs. Anyway, you can download the "packmol" program (). Simple
and easy for this kind of stuff (I use it a lot).
The only problem is on the last line of the .pdb file it generates it
will put zeroes instead of the box size.
Also, it will not add hydrogens to the protein molecule, so add them first.
Hope it helps.
On 4/27/06, Erik Marklund <erikm at xray.bmc.uu.se> wrote:
> 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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