Hi, What you have described is no physical. You should avoid doing that unless you have a better reason. In normal MD, counter ions don't need special treatment such as restraint to some solute.
Regards Terry > On 3 May 2016, at 9:51 PM, soumi <soum...@rediffmail.com> wrote: > > Dear > All, > I am working on MDsimulation of Protein-DNA complex using AMBER99SB-ILDN > force field with gromacs.In order to neutralize the net charge on the > protein-DNA complex by adding the correct number of positive ions or > negative ions I have used the following command in gromacs > gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -np > 38 > When prompted, I choose group 13 "SOL" for embedding ions because I > do not want to replace parts of protein-DNA complex with ions.In MM > optimisation process for solvated complex,counter ions are easily separated > from the solute .Such separated ions have no function as a counter ion.In > order to avoid such situation I desire the positions of Na+ ions around DNA > to be constrained within 5 A from the PO4- groups of DNA backbone,while the > Na+ ions around protein were contrained within 6 A from the carbon atom > of the carboxyl group of the negatively charged Asp 129 residue.How can the > positions of Na+ ions around DNA be constrained within 5 A from the PO4- > groups of DNA backbone by which command or method using gromacs > exclusively (not AMBER TOOL /AMBER PACKAGE )?With Regards ,Soumi Das > -- > 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. -- 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.