Link groups with make_ndx

User discussions
1

I have generated a large number of groups through the gmx select command, now I need to link all these groups into one. Somebody can help me? Thanks!

2

Use -on to output the selections to an index file:
gmx select -on index_output.ndx

Then you can combine them using make_ndx with the | (or) function:
gmx make_ndx -n index_output.ndx -o index_combined.ndx

3

Thank you…but i have more than 12000 groups. Or is not usefull in this case.

4

With this many groups, I suggest trying to find a way to make fewer groups; there has to be a way to express your selections more generally so you don’t have to deal with so many.

5

Thanks! We solved this problem. mm

6

Could you please share what your solution was? That is the purpose of this forum. Other users may find it useful in the future to know what you did.

7

Hi!!
A collaborator wrote a code that links all groups into one. I ´ll ask him to share the program, MM

8

Hi!!
Here we share the script to link several groups avoiding redundance:

MergeGroups script

This script reads a ‘ndx’ file (INPUT) from GROMACS containing many groups of atoms,

and writes-out a single merged file (OUTPUT) with non-redundant atom numbers.

To run: 1) modify in lines 1 and 2 INPUT & OUTPUT names;

2) modify in line 3 the text in the OUTPUT header: [ group of …];

3) execute this script from the command line.

Diego Guerin; June 2020

export INPUT=IndexMut17_wat4ALYR.ndx
export OUTPUT=IndexMut17_wat4ALYR_mrg.ndx
echo [ group of TIP3 that reach a 4A distance from LYR] > $OUTPUT
awk ’ BEGIN {imin=1; imax=500000}
{for (i=1; i<16; i++) A[$i]=$i}
END { for (j=imin; j<imax+1; j++) {
if (A[j] > 0)
{k=k+1; if (k<15) printf " %5d", A[j]
else {printf " %5d\n", A[j]; k=0}
}
}
}’ $INPUT >> $OUTPUT