[gmx-users] Water molecules fill in gaps in protein

[Dawid das]

Dear Gromacs Users,

I noticed that quite often after adding the solvent (water) to the protein,
the water
molecules fill in gaps inside the protein which are not occupied.
I am afraid that since their position may not be optimal (they actually
should not
be there), it will lead to artifacts as the MD simulation progresses.
What is your opinion on removing these water molecules on some occasions?

Best wishes,
Dawid Grabarek