[gmx-users] Two questions about index files

Andrew DeYoung adeyoung at andrew.cmu.edu
Sun Jul 8 21:59:38 CEST 2012


I hope that all is well. If you have time, I have two questions about index

(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?

(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:


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!

Andrew DeYoung
Carnegie Mellon University

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