Hi:
Thank you for the advice and assistance...I'll work through some of the equations some more. My current thought is that I can get it to work using either a static lambda or a gradient, as long as I'm careful about the bookkeeping. Perhaps I can put together a test run by patching some TI runs together prior to modifying the code. I'll dig into the technical side a bit more, and try to come up with a good plan.
Cheers, Jerome
-----Original Message-----
From: Carlos Simmerling [mailto:carlos.simmerling.gmail.com]
Sent: Wednesday, December 01, 2010 1:48 PM
To: AMBER Mailing List
Subject: Re: [AMBER] (no subject)
one might be able to do it using the TI functionality and stepping the
lambda... but I'm not sure.
On Wed, Dec 1, 2010 at 4:20 PM, Nilmeier, Jerome P. <nilmeier1.llnl.gov>wrote:
> Hello:
>
> I am interested in applications very similar to what a steered md run might
> provide, but with alchemical parameters as the time varying function. I am
> just now learning the details of Amber, and I thought that maybe there would
> be a way to generate these types of trajectories using existing machinery.
> Perhaps we can talk more about it when you have time?
>
> Best, J
>
> -----Original Message-----
> From: Adrian Roitberg [mailto:roitberg.qtp.ufl.edu]
> Sent: Wednesday, December 01, 2010 8:10 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] (no subject)
>
> I am pretty sure there is no code like that in amber, but I would be
> VERY interested in why you would do such a thing.
>
> Adrian
>
> On 12/1/10 5:05 PM, case wrote:
> > On Tue, Nov 30, 2010, Nilmeier, Jerome P. wrote:
> >
> >> I am interested in generating trajectories whereby an alchemical
> >> potential is continuously altered over the course of the trajectory.
> >> (Something like steered MD, but with lambda varying rather than a
> >> biasing potential). Is there a straightforward way to do this?
> >
> > I'm pretty sure there is no current way to do this, unless Volodymyr
> stuck
> > something in the ABMD stuff that I missed....
> >
> > ...dac
> >
> >
> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> --
> Dr. Adrian E. Roitberg
> Associate Professor
> Quantum Theory Project, Department of Chemistry
> University of Florida
>
> Senior Editor. Journal of Physical Chemistry.
>
> on Sabbatical in Barcelona until August 2011.
> Email roitberg.ufl.edu
>
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Received on Wed Dec 01 2010 - 14:30:04 PST
