[gmx-users] Re: gro does not match top

[Shima Arasteh]

Thanks!
I did! :-)





Sincerely,
Shima


________________________________
From: Mark Abraham <mark.j.abraham at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Cc: Shima Arasteh <shima_arasteh2001 at yahoo.com> 
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 <jalemkul at vt.edu> 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