[gmx-users] Running gromacs analysis on a HPC

Pandya, Akash akash.pandya.15 at ucl.ac.uk
Tue Jun 11 16:52:20 CEST 2019

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.


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