[gmx-users] Two questions about index files

[Justin A. Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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