[gmx-users] toluene as a slovent

[Mijiddorj B]

I recommend you to use (1) gmx insert-molecules tool to fill the box that
solvent molecule. For the number of molecules, you can use as much as a
higher number using -nmol option. The result tells you, how many molecules
inserted from ordered numbers. (2) Then, you should manually edit the
topology file using the correct number of toluene.


>
> ------------------------------
>
> Message: 5
> Date: Mon, 2 Dec 2019 12:14:21 +0330
> From: Iman Katouzian <imaneternity at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] toluene as a slovent
> Message-ID:
>         <CALipc=ovOtQ9Fq0SXpBRoe=
> ffcoDUoQOGukzUUwcb_+tAmOOpw at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hello,
>
> I have downloaded the toluene pdb file and want to use it as solvent in
> GROMACS rather than the water molecules. I have added toluene as a molecule
> using gmx solvate -cs toluene.gro however, in the next steps, it is not
> added to the topol.top file and I cannot go-ahead to the next steps of
> simulation. I'd be grateful if someone can help me with this issue as I
> have not tried other solvents rather than water before.
>
> Thanks.
>
> On Sun, Dec 1, 2019 at 4:04 PM Iman Katouzian <imaneternity at gmail.com>
> wrote:
>
> > Hello,
> >
> > I have downloaded the toluene pdb file and want to use it as solvent in
> > GROMACS rather than the water molecules. I have added toluene as a
> molecule
> > using gmx solvate -cs toluene.gro however, in the next steps, it is not
> > added to the topol.top file and I cannot go-ahead to the next steps of
> > simulation. I'd be grateful if someone can help me with this issue as I
> > have not tried other solvents rather than water before.
> >
> > Thanks.
> >
> > --
> >
> > *Iman Katouzian*
> >
> > *Ph.D.** candidate of Food Process Engineering*
> >
> > *Faculty of Food Science and Technology*
> >
> > *University of Agricultural Sciences and Natural Resources, Gorgan, Iran*
> >
>
>
> --
>
> *Iman Katouzian*
>
> *Ph.D.** candidate of Food Process Engineering*
>
> *Faculty of Food Science and Technology*
>
> *University of Agricultural Sciences and Natural Resources, Gorgan, Iran*
>
>
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