[gmx-users] genion

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Jun 19 08:27:27 CEST 2008

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.



On Thu, Jun 19, 2008 at 6:24 AM, shahrbanoo karbalaee
<shahrbanoo at gmail.com> 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
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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
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