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 <imanetern...@gmail.com> > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] toluene as a slovent > Message-ID: > <CALipc=ovOtQ9Fq0SXpBRoe= > ffcoduoqogukzuuwcb_+tamo...@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 <imanetern...@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* > > > ------------------------------ > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > End of gromacs.org_gmx-users Digest, Vol 188, Issue 3 > ***************************************************** > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
