[gmx-users] solvate with an exact number of solvent molecules

[Mark Abraham]

Hi,

You should gmx insert-molecules a single-molecule file (-ci) into whatever
solvated or unsolvated box (-f) makes sense. Don't insert a solvated box!

Mark
On 02/03/2015 10:25 pm, "Rebeca García Fandiño" <regafan at hotmail.com> wrote:

> Thanks a lot for the suggestion, Jennifer.
> However, using gmx insert-molecules you cannot use the equilibrated
> solvent box, is it OK? I assume "your_insert.gro" should be a single
> molecule of solvent, right? I have tried using the whole box, and it does
> not work.
>
> Best wishes,
>
> Rebeca.
>
> Dr. Rebeca Garcia
> Santiago de Compostela University
> Spain
>
> Hi Rebeca,
> In GROMACS 5.0,  I use
> gmx insert-molecules -f your.gro  -ci  your_insert.gro -o output.gro -nmol
> xxx
> where xxx is the number you want.
> Hope it helps.
> Jennifer
>
> On Mon, Mar 2, 2015 at 6:44 PM, Rebeca García Fandiño <regafan at
> hotmail.com>
> wrote:
>
> > Dear GROMACS users,
> > I am trying to do a systematic study using GROMACS and I would like to
> > have the same number of solvent molecules in all my systems. Using gmx
> > solvate in GROMACS 5.0 it is only possible to select the maximum number
> of
> > molecules in the box, but not a concrete number.
> > Does anyone knows about any way to solvate a molecule selecting an exact
> > number of solvent molecules in the box?
> > Thanks a lot in advance.
> > Best wishes,
> > Rebeca.
> >
> > Dr. Rebeca Garcia
> > Santiago de Compostela University
> > Spain
> >
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