H-H bond in TIP3 water

From: Jorge Pikunic (jorge.pikunic_at_bioch.ox.ac.uk)
Date: Mon Aug 01 2005 - 17:21:26 CDT


Is "auto none" required to build water segments? or not anymore?

According to the NAMD user's guide, it is required

"The residue type for water depends on the model, so here we alias HOH
to TIP3. Because CHARMM uses an additional H-H bond we must disable
generation of angles and dihedrals for segments containing water. Then
read the pdb file.
# (7) Build water segment
pdbalias residue HOH TIP3 ; # formerly "alias residue ..."
segment SOLV {
 auto none
 pdb output/6PTI_water.pdb
} "

But according to these posts, it is not required:
"If you're going to be running your simulation in NAMD, it's safe to
edit the topology file and remove the H1-H2 bond. NAMD will ignore it
anyway, since it doesn't need the bond to do rigid waters, and your
VMD images will look better."

Which of the two versions is true? It seems that the user's guide is not
updated. Or am I misinterpreting something?

Please help :) Thank you!


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