Thanks! I did! :-)
Sincerely, Shima ________________________________ From: Mark Abraham <[email protected]> To: Discussion list for GROMACS users <[email protected]> Cc: Shima Arasteh <[email protected]> Sent: Sunday, March 24, 2013 9:50 PM Subject: Re: [gmx-users] Re: gro does not match top On Sun, Mar 24, 2013 at 2:32 PM, Justin Lemkul <[email protected]> wrote: > >On 3/24/13 9:02 AM, Shima Arasteh wrote: > >In fact the genion does not add the neutralizing CL ions to gro file! Why? >>How can I solve this problem? >> >> > Using -nn and -conc is probably incompatible, because -conc will add some number of ions, which may not play nicely with the fact that you are then manually saying "add only 3 negative ions" with -nn 3. The correct formation of the command is to use genion -conc 1 -neutral. > If Shima had read genion -h, there is a description of -conc that announces that it overrides -nn and -np. Mark -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
