Re: [AMBER] Lambda Exchange

From: Jason Swails <>
Date: Wed, 08 Oct 2014 15:29:53 -0400

On Wed, 2014-10-08 at 13:50 -0500, Jeff Wereszczynski wrote:
> Hi Jason,
> OK, I'll disable the error checking and proceed with caution :)

Indeed. I can tell you that _I_ think it should work, for whatever
that's worth :).
> And yes, the thermodynamic cycle works perfectly fine if you scale
> intramolecular non-bonded interactions as well as intermolecular
> interactions.

I imagined it was, but couldn't convince myself of that just by thinking
about it for a few minutes.

> The reason I ask is that in some systems it can help convergence if
> you left the intramolecular interactions on, since this represents a
> smaller perturbation to the system. Most of the time removing the
> intramolecular interactions should be fine though, but I wanted to
> ask.

Makes sense.

All the best,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed Oct 08 2014 - 13:00:02 PDT
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