Distance between atom(s) in a protein and waters during a simulation

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Hi!

Could someone guide me how to extract the following from a trajectory:

  1. Every water atom (including both the atomnr and resnr) within a specified distance from “probe atom(s)” for every specified snapshot.

  2. Every pairwise distance(s) for every snapshot. I have extracted a ndx-file with the wanted atomnr of the waters for every snapshot using gmx select (gmx select -f …/pr-10ns.xtc -s …/pr-10ns.tpr -n …/Dr.ndx -pbc yes -select “resname TIP3 and within .5 of atomnr 1326” -on test.ndx -dt 500), but I don’t know how to get the corresponding distances.

I have also tried to extract stripped pdb files from the trajectories, to be able to calculate the distances from the coordinates, but I only get a pdb from the first snapshot when using gmx select (gmx select -f …/pr-10ns.xtc -s …/pr-10ns.tpr -n …/Dr.ndx -pbc yes -select “resname TIP3 and within .5 of atomnr 1326” -pdbatoms selected -ofpdb pdb-test.pdb).

Kind regards,

Marcus