Hello Alex,
What works for me is setting '$i' within singe quotation marks, e.g.,
'group '$i' and name C10 plus group '$i' and name C20'
Note that this is more of a bash escaping quotes issue and only a GROMACS issue insofar as the selection syntax requires
the quotes.
Best,
Christian
On 11/6/19 3:32 AM, Alex wrote:
Dear all,
Could one kindly let me know how $i should come in gmx gangle used in a for
loop to avoid syntax errors?
I tested different flavors like "$i", "${i}", ..., and still the problem is
here.
#!/bin/bash/
for i in {1..1000}
do
gmx gangle -g1 vector -group1 'group $i and name C10 plus group $i
and name C20' -g2 vector -group2 'cog of group 0 plus cog of group $i' -n
ind.ndx -f ind.xtc -s ind.tpr -oav aver$i.xvg -oh hist$i.xvg
done
Thank you
Alex
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