[gmx-users] Two questions about index files

Justin A. Lemkul jalemkul at vt.edu
Sun Jul 8 22:05:18 CEST 2012

On 7/8/12 3:59 PM, Andrew DeYoung wrote:
> Hi,
> I hope that all is well. If you have time, I have two questions about index
> files:
> (1) Do you know if there is a limit on the number of entries an index file
> can have? I am trying to write a shell script which would allow me to run
> g_traj 200000 times, feeding a different index entry to it on each
> iteration. This is because I have used g_select to (dynamically) pick out
> atoms that meet certain criteria. I have 200000 time steps in my trajectory,
> so I have 200000 entries in my index file. I will try this, but do you have
> any experience with this about whether such a large index file will work?

The only limitation here is disk space and available memory, both of which are 
external to Gromacs.

> (2) Normally, when I call any Gromacs program with the -n switch, the
> program prints to the screen all of the choices available in the index file.
> I am planning to use the "<<EOF" method for making this choice
> non-interactive, as described here:
> http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts#Withi
> n_Script
> This works, but the problem is that the program still prints all of the
> index file selections to the screen, even though the input is now automated
> from the shell script. This means that the program insists upon printing out
> all 200000 index selections on each of my 200000 calls to the program, and
> this can take a lot of time.  Do you know if there is a way to suppress the
> printing of the index files selections and somehow feed input to the program
> in the background/invisibly? Simply putting & at the end of the command does
> not seem to work.
> In other words, is there a way to make commands non-interactive _in the
> background_?  Thank you!

I don't think so.  There is a hidden option called -quiet that reduces some 
screen output, but since selections are dependent upon user choice, they can't 
be suppressed, at least in the quick trials I just did.  I suppose you could 
modify the source to prevent this printing, but whether or not that's worth the 
effort is up to you.



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


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