Dear Tsjerk and Mark Thanks for your time and attention.
using g_select -f *.xtc -s *.tpr -n index.ndx -oi -select '"Close to Protein" resname SOL and within 0.25 of group Protein' solved my problem. I want to use trjorder -f *.xtc -s *.tpr -n index.ndx -o ordered.pdb -nshell -r 0.25 -na 3 -da 1 to order water molecules according to the smallest distance to atoms in a reference group (protein). Should the results of both of g_select and trjorder be the same? Best regards.
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