Re: [AMBER] Hydration Free Enery by TI

From: <>
Date: Tue, 19 Mar 2013 07:00:39 -0400 (EDT)


> ... so, you mean that I don't really need to do the "in gas phase" step to
> close the thermodynamic cycle???

you dont need to do the vdw-step of the vacuum transformation...

> When you say that I need to do the vacuum charge removal for the solute,
> you mean in vacuo?

...but you do need to do the charge removal in vacuum for the two-step

> And then, if I wish to avoid this step (the in vacuo), should I do the
> one-step (charges + van der Waals) transforation in explicit solvent?

...and you can leave out the vacuum steps completely when switching to
one-step transformations.

Kind Regards,


Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Tue Mar 19 2013 - 04:30:02 PDT
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