[gmx-users] Analysis using sh file

[Alessandra Villa]

Hi,

On Tue, Feb 4, 2020 at 11:14 AM <ric.concu at gmail.com> wrote:

> Dear all,
>
>
>
> I have recently upgrade my Gromacs to the 2019 version from the 5.0.4
>
>  and I found out that now that while I'm trying to use a .sh, as I was
>
>  doing in the version 5.0.4, now I'm receiving back an error since the
>
>  syntax is wrong. I'm wondering if someone could please help me.
>
>
>
>
>
> This is an example of a line I have been using on Gromacs 5.0.4:" echo "10"
> "12" | gmx rdf -f box_tot -s box-npt -n box -o Mol1 &"
>
> and this is the error message I'm receiving from Gromacs: "Error in user
> input: Invalid selection '10 12 '   Near '12'      syntax error
>
>
You could use the option -ref and -sel  (see
http://manual.gromacs.org/documentation/current/onlinehelp/gmx-rdf.html?highlight=gmx%20rdf
)

In your case the command will be

gmx rdf -f box_tot -s box-npt -n box  -ref 10 -sel 12 -o Mol1

Best regards
Alessandra


>
> Regards,
>
> Riccardo
>
>
>
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