Thanks for your prompt replay. I thougnt it would be more elegant way to do it using the commands. If not that is what I am going to do. Best, Netaly
On Mon, Nov 13, 2017 at 2:37 PM, Hermann, Johannes < j.herm...@lrz.tu-muenchen.de> wrote: > Hi Netaly, > > one way would be to calculate the number of Na, Cl, and Mg ions by hand, > i.e. with the box size and the respective concentrations, and add the > correct amount of ions in two steps, with the flags -np or -nn. E.g. in the > first step you add Na and Cl and in the second you add Mg. > > All the best > > Johannes > > > On 13.11.2017 13:31, Netaly Khazanov wrote: > >> Dear Gromacs User, >> >> Is it possible to simulate system with two salt concentrations , e.g. NaCl >> 0.1 mol/L and MgCl2 0.002 mol/liter? >> >> The commands that i am using you can see below: >> >> grompp_d -f ions.mdp -c ligand_MG_box_water.gro -p topol.top -o ions.tpr >> genion_d -s ions.tpr -o ligand_box_water_NaCL.gro -p topol.top -pname NA - >> nname CL -neutral -conc 0.1 >> grompp_d -f ions.mdp -c ligand_box_water_NACL.gro -p topol.top -o ions.tpr >> genion_d -s ions.tpr -o ligand_box_water_NaCL_MgCl2.gro -p topol.top >> -pname >> MG -pq 2 -nname CL -neutral -conc 0.002 >> >> The message that I got after the execution of the last command is :"No >> ions >> to add and no potential to calculate." >> >> Is it right way to do it? >> Thank you in advance. >> Netaly >> >> >> > -- > ______________________________________ > *Technische Universität München* > *Johannes Hermann, M.Sc.* > Lehrstuhl für Bioverf > <https://maps.google.com/?q=uhl+f%C3%BCr+Bioverf&entry=gmail&source=g> > ahrenstechnik > Boltzmannstr. 15 > D-85748 Garching > Tel: +49 8928915730 > Fax: +49 8928915714 > > Email: j.herm...@lrz.tum.de > http://www.biovt.mw.tum.de/ > > -- > 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. -- Netaly -- 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.