[gmx-users] How to automate genion completely?

Justin A. Lemkul jalemkul at vt.edu
Sun Mar 25 03:54:33 CEST 2012

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!), 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.

Groups can be chosen by name, and passed via 'echo' like other commands.  See 
http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts.  Thus 
you can use something like

echo SOL | genion -s topol.tpr



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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