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

[Mark Abraham]

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