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Merge pull request #72 from DanielChau128/patch-1
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Update Gromacs documentation link for specifying selections from command line
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heatherkellyucl committed Jun 18, 2024
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Expand Up @@ -622,7 +622,7 @@ gerun gmx_mpi -v -stepout 10000

#### Passing in options to GROMACS non-interactively

Some GROMACS executables like `trjconv` normally take interactive input. You can't do this in a jobscript, so you need to pass in the input you would normally type in. There are several ways of doing this, mentioned at [GROMACS Documentation - Using Commands in Scripts](http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts). The simplest is to echo the input in and keep your gmx options as they would normally be. If the inputs you would normally type were 3 and 3, then you can do this:
Some GROMACS executables like `trjconv` normally take interactive input. You can't do this in a jobscript, so you need to pass in the input you would normally type in. There are several ways of doing this, mentioned at [GROMACS Documentation - Specifying selections from command line](https://manual.gromacs.org/2021/onlinehelp/selections.html#specifying-selections-from-command-line). The simplest is to echo the input in and keep your gmx options as they would normally be. If the inputs you would normally type were 3 and 3, then you can do this:

```
echo 3 3 | gmx whatevercommand -options
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