[gmx-users] How to automate genion completely?

Mark Abraham Mark.Abraham at anu.edu.au
Sun Mar 25 13:15:52 CEST 2012

On 25/03/2012 12:43 PM, John Ladasky wrote:
> I am starting to write my own turnkey scripts to automate GROMACS (v 
> 4.5.4) work flow.  Many of the GROMACS commands, such as pdb2gmx and 
> genion, have interactive options by default, meaning that you manually 
> enter information when the program runs.
> In the tutorials, we are taught to invoke pdb2gmx from the command 
> line using certain arguments which name input and output files.  But 
> then, we choose our force field from a numbered menu inside pdb2gmx.  
> However, if you know the name of the force field (these names SHOULD 
> be listed somewhere!),

Sure, you can find them the same place pdb2gmx does - as ${name}.ff 
directories in working directory or under $GMXLIB.

> you can use the "-ff" argument when you call pdb2gmx from the shell.  
> For example, "-ff gromos45a3".  Then you do not have to manually enter 
> anything.
> I am looking for a corresponding option for genion.  Genion offers a 
> numbered menu to ask you which group of atoms you wish to use for ion 
> replacements.  The groups that most of us would want to use are the 
> "Water" or "SOL" groups.  With the files that I'm working with right 
> now, these pop up as groups #12 and #13, respectively.  But they 
> needn't always be numbered this way, if the user has altered the 
> standard .ndx file.
> Is there an argument that one can supply to genion from the command 
> prompt which will select the replacement group automatically, as "-ff" 
> selects a force field for pdb2gmx?  I have the v. 4.5.4 manual.  I do 
> not see the argument (pp. 273-4).  I hope that it exists, and that it 
> is just undocumented.

That does seem to be a gap in the manual. I've expanded the discussion 
in section 8.1 of the manual to include:

+Each tool that can use groups will offer the available alternatives
+for the user to choose. That choice can be made with the number of the
+group, or its name. In fact, the first few letters of the group
+name will suffice if that will distinguish the group from all others.
+There are ways to use Unix shell features to choose group names
+on the command line, rather than interactively. Consult the GROMACS
+webpage for suggestions.


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