Tsjerk,

Thanks for your reply.  I have tried using the center option, but ran into
similar problems.  Here are the exact commands that I used:

g_select -f file.xtc -s file.tpr -n index.ndx -select 'group 14 and within
0.71 of group 13' -b 37.875 -e 37.875 -on index1 (where group 14 contains
the water molecules and group 13 is the solute molecule)

trjconv -s file.tpr -n index1.ndx -f file.xtc -o out.gro -b 37.875 -e 37.875

trjconv -f out.gro -s file.tpr -n index.ndx -o out2.gro -center

Does this procedure seem reasonable?

Thanks,
Blake

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