Hi Prof Case,
I have a question …
When you stated “But this uses the old (before soft-core) approach that requires dummy
atoms, and illustrates reasons why this is no longer the recommended
approach…”
Could you elaborate a bit on the soft-core approach versus the conventional dummy atom approach?
I know I will find details in the published literature of TI, but if you could give a basic idea of these approaches, it will very useful to a lot of people in the field.
Thanks
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________________________________
From: David Case <david.case.rutgers.edu>
Sent: Thursday, October 3, 2019 3:59:54 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Thermodynamic integration
On Thu, Oct 03, 2019, Debarati DasGupta wrote:
>Is it not that when I say “not exist” it denotes void space. Can we have
>void space in our simulations? Isnt it unrealistic?
It is more precise to say that the "dummy" ethanol molecule is decoupled
from its environment: the ethanol molecule is still "there" (it has
coordinates in the restart files), but it has no interactions with the
rest of the system, and so is a sort of "ghost".
At the end point, other solvent molecules will generally fill in the space
that used to be occupied by the ethanol. So there will be no "void
space".
...hope this helps....dac
p.s.: there is a "toluene -> nothing" transformation tutorial here:
http://ambermd.org/tutorials/shirts/index.html
But this uses the old (before softcore) approach that requires dummy
atoms, and illustrates reasons why this is no longer the recommended
approach. But it still covers the basic ideas of these sorts of
simulations.
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Received on Wed Oct 09 2019 - 12:00:03 PDT
