Currently, I am working on an HPC cluster and I submit jobs instead of directly executing the Gromacs commands. However, by default it asks for input from the user on terminal, which I am unable to do since it is hidden from me. So, I want to know if there is a way to auto-input the user inputs or tweak the parameters to do so?
As far as I know all parameters like e.g. selections can be made from the command line while launching the respective tool. All available option can be seen with the "-h" flag.
http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
say you need to add ions and then select SOL automatically, it can be done in single line using 'echo' command,
echo SOL | gmx genion -s ions.tpr -o ions.gro -p complex.top -pname NA -nname CL -conc 0.1
for more details, you can look in to Justins answer.
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