Dear community,
I've recently been running some thermodynamic integration simulations in
AMBER. I also noticed the keyword 'dielc' is compatible with TI. The
description of 'dielc' in AMBER manual says 'It is implemented by scaling
all of the charges by sqrt (dielc)'.
I was wondering what energy the keyword 'dielc' scales and calculates. Does
it conclude the protein-protein, protein-ligand, protein-water, and also
water-water interactions if we're now looking at a system containing a
protein and a ligand?
I was also wondering if there's any keyword that can be used in TI
simulation to only scale the charges inside the soft core region.
Thanks so much for your help.
Best,
Fanyu
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Received on Sat Jan 20 2024 - 04:30:02 PST
