[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
> 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
you can use something like
echo SOL | genion -s topol.tpr
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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