Dear Gromacs users, I have a modelled protein whose net charge is +12.69, and I would like to ionize the protein to make it neutral using genion command, but in genion command we can add a specific number of postive or negative charged ions which for my case would not completely neutralize the system and i learnt from Justin tutorial that we can even neutralize it using -conc and -neutral options in conjugation. As I am running a membrane-protein simulation, I would like to know the command which I am using is correct or not.
genion -s ions.tpr -o protein_solv_ions.gro -p topol.top -pname NA+ -nname CL- -nn 12 -neutral If my command is wrong Please suggest the right one as In future i have to conjugate SOL and CL- ions to create a special index file. Thanks Ram
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
