Re: [AMBER] TI calculation: viewing lambda trajectories that are not 0 or 1 - (writing parm files)

From: <>
Date: Thu, 6 Jan 2011 05:36:49 -0500 (EST)


I'm not perfectly sure what you mean, but my guess is the answer is no.
Due to the dual topology model, Amber will propagate both sets of atomic
coordinates in parallel, there is no such thing as 20% of a coordinate. So
your end state prmtop files will work on the crd-files at any lambda from
zero to one.

You can visualize your trajectories in VMD of course, you will see atoms
behaving as if they only feel e.g. 20% of the interaction strength they
had at the initial state.

Kind Regards,


On Thu, January 6, 2011 2:02 am, g t wrote:
> Hi,
> Is there any way to get amber to write a parm file that represents the
> structure used for lambda points between 0 and 1, (e.g. 0.., 0.2, etc)?
> That
> way, the trajectory could be visualised in a viewer such as chimera or
> VMD.
> The reason I am enquiring about this is that I am interested in preparing
> a
> series of graphics that explain the lambda concept to people unfamiliar to
> it in presentations, etc.
> Cheers!
> GT
> _______________________________________________
> AMBER mailing list

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

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Received on Thu Jan 06 2011 - 03:00:04 PST
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