[gmx-users] How to automate genion completely?

John Ladasky blind.watchmaker at yahoo.com
Sun Mar 25 03:43:45 CEST 2012

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.

Thanks, as always.

More information about the gromacs.org_gmx-users mailing list