Re: [AMBER] Sander and Thermodynamic integration and softcore

From: David A Case <>
Date: Fri, 26 Oct 2018 08:06:55 -0400

On Thu, Oct 25, 2018, Khabiri, Morteza wrote:
> Currently, I am trying to use thermodynamic integration in the sander,
> however, I would like to start my confirmation with different charge and
> vdw parameter as in the forcefield. Imagine I want to go from state A to
> state B using softcor potential. So I would like to start state A (at
> lambda zero) with the half of the charge of stateB or lambda=1.
> Is there any idea how can I start from some desire values for
> vdw/charges/.. with soft core and end with real values?

In free energy simulations, you have two end states, called "A" and "B".
You can prepare them however you want, and parmed is often helpful if
you want to make changes to an existing prmtop file. Or, if you need to
change lots of things, you may need to write a script to modify the
prmtop files in the way you want.

The code doesn't care where the charges you assign to state A came from,
or what they represent. So, if you want charges in state A to be half
those in state B, just go ahead and prepare you prmtops in that manner.
(Of course, the question of what to do with the resulting free energy
values is up to you as well.)

...hope this helps....dac

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Received on Fri Oct 26 2018 - 05:30:02 PDT
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