[gmx-users] Running gromacs analysis on a HPC

[John Whittaker]

Hi Akash,

Take a look here:
http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts

Alternatively, I think you could also do something like:

echo "1" > select; echo "12" >> select;

gmx rdf -s proteinwater.tpr -f proteinwater.xtc -o proteinwaterrdf.xvg
-bin 0.002 -norm rdf -selrpos whole_res_com < select

and that will work.

Cheers,

John

> Hi all,
>
> I am trying to run gmx rdf on a HPC via a script. This is the command I am
> using :
>
> echo 1 12 | gmx rdf -s proteinwater.tpr -f proteinwater.xtc -o
> proteinwaterrdf.xvg -bin 0.002 -norm rdf -selrpos whole_res_com
>
> 1 being the protein and 12 being the water
>
>
> I get this error:
>
> Program:     gmx rdf, version 2018.2
>
> Error in user input:
> Invalid selection '1 12 '
>   Near '12'
>     syntax error
>
> For more information and tips for troubleshooting, please check the
> GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> Please can you advise me on how I can sort out this issue.
>
>
> Akash
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