[gmx-users] RE: g_rdf

[Mark Abraham]

Junfang.Zhang at csiro.au wrote:
> Hi Erik,
> 
> Thank you very much for your reply.
> 
> When I use
> 
> g_rdf -f traj.xtc -n index.ndx
> 
> to analyze the radial distribution around a specific set of particles, I
> have to choose the groups manually 

I don't know anything about g_rdf, but perhaps you should be using an 
index file to describe the specific set of particles. You can edit these 
by hand in a text editor.

> and sometimes there is an error
> message like "time limits exceeded". Can you please let me know how to
> put the choices in a script file which I can submit by using command
> "qsub  filename"?

To solve this problem in general, the tool you want is called "expect". 
It allows you to run a command like "expect expect_script.tcl" (which 
you can put in a shell script to keep qsub happy) which itself runs 
"g_rdf -f traj.xtc -n index.ndx". Now the expect program gives 
pre-determined responses to the sub-program's prompts. In simple cases, 
you can use the related program autoexpect to watch you interact with 
the program and come up with an expect_script.tcl that should reproduce 
the way you interacted when you were teaching it. I use expect scripts 
to automate my interactions with pdb2gmx, for example.

Expect is probably installed on recent *NIX distributions (or at least 
those on which the scripting language Tcl is installed), but visit 
http://expect.nist.gov for source code, examples, help, etc.

Mark