Gmx analysis on multiple directories

User discussions
1

I ran simulations for multiple systems with same method; saved into different directories. I want to do same data analysis (gmx rms, cluster, hbond…) in all these directories. Is there a way to simultaneously apply a gmx command on multiple directories?

Thank you,
Neena

2

Hi Neena,
I wrote a script with loops, and set the directories and file names as variables.
In the loop, there were gmx commands.

Hope it helps.
Best,
Anh

3

Bash scripting will do the hack,

for dir in dir_1 dir_2 dir_n;
do 
    cd $dir
    gmx rms/cluster/hbond .....
    cd ..
done

You might want to use echo n | gmx for non-interactive user input. Here n is user choice (if any) . You can echo multiple times ( e.g., echo n1 n2 | gmx)

Best,
Masrul