Hi sh-karbalaee, Well, running an MD simulation has nothing to do with genion per se. But it's better not to have a net chare in your system. Therefore you'd best add an ion (at the least) to your system with unit charge. Whether you do that using genion or do it by hand, is entirely up to you. Check the archives of the user list and the wiki... Counterions and charged systems have been discussed often.
Cheers, Tsjerk On Thu, Jun 19, 2008 at 6:24 AM, shahrbanoo karbalaee <[EMAIL PROTECTED]> wrote: > Dear justin > thanks for reply about g_dist. > about genion for peptides.Do I must use command genion for MD > peptides with one charge(13 aa)?Is it necessary for md? > > best > sh-karbalaee > _______________________________________________ > 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 > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ 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
