GROMACS version: 2018.3
GROMACS modification: No
I try to extract the coordinates of hydration water molecules of a protein, which are assumed to be 0.3 nm from the protein surface atoms.
I used the following command:
gmx select -f md01.xtc -s md01.tpr -b 0 -e 0 -select ‘group Protein or (group “SOL” and same residue as within 0.3 of group “Protein”)’ -ofpdb test.pdb -pdbatoms selected
This gives properly what I expected (Left image of the attached file).
However, when I try to do the same thing in another frame (here, it is 5000th frame),
gmx select -f md01.xtc -s md01.tpr -b 5000 -e 5000 -select ‘group Protein or (group “SOL” and same residue as within 0.3 of group “Protein”)’ -ofpdb test.pdb -pdbatoms selected
it gives a strange results, where water molecules that are very far from the protein surface (beyond 0.3 nm) were selected (Right image of the attached file).
I would like know how I can get the similar result to the first example (frame0) for other frames.
I confirmed that in the trajectory, there exist lots of water molecules surrounding the protein at the 5000th frame, but these water molecules are not selected…