On Sat, Jan 20, 2024, Fanyu Zhao via AMBER wrote:
>
>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.
As the message indicates, all this (very, very ancient) option does is
scale all of the charges. If you have an explicit water system, this will
change the behavior of the system so drastically that is a little hard to
think of a case where it would be very useful, since it affects *all*
electrostatic interactions.
>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.
Parmed could do this for you, creating a new prmtop file that changes
charges in any manner you want. Type "help change" at the parmed prompt.
....dac
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Received on Sat Jan 20 2024 - 15:30:02 PST
