Dear Amber users!
I am using the following cpptraj workflow to remove periodic boundary
conditions for a dimeric protein bound to a ligand, to
analyze water-mediated hydrogen bonding during molecular dynamics. My
system contains protein, ligand, water, and ions, and I want to keep
everything in the post-processed, with the protein properly centered:
unwrap bymol
unwrap :* # sometimes used only for protein residues
autoimage
image origin center familiar
center :*.N,CA,C origin # center on backbone atoms
# rms first :*.N,CA,C-\n # optionally add rms fit
Visually, this creates a reasonable system without jumps across box.
However, when I visualize water near the ligand,I notice that water
molecules appear to move very rapidly in a non-physical way. How could it
be fixed?
Many thanks in advance!
Enrico
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Received on Wed Jan 21 2026 - 15:30:02 PST
