Hi Mark, I think, it is not a chemistry question exactly. Genion command asks for a group whose atoms are replaced with ions. I have no solvent molecules in my system. In this respect, how can I incorporate ions into my system?
Thanks Ozge -----Original Message----- From: "Mark Abraham" <[EMAIL PROTECTED]> To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> Date: Thu, 18 Oct 2007 16:49:15 +1000 (EST) Subject: Re: [gmx-users] Addition of ions in vacuum simulations > Hi all, > > I am simulating a charged peptide in vacuum. I want to neutralize my > system by using genion command,and as expected it asks me a continuous > solvent group for the replacement; however, I have no solvents. > > How can I add ions to my system if I am in vacuum? or Is it necessary to > add ions while performing simulations in vacuum? This is a chemistry question that will depend on your protein and what you're trying to study. In some cases you might also consider modifying the chemical groups so that there is not an ion there. Mark _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
