AMBER Archive (2006)

Subject: Re: AMBER: Calculate interaction energy between small organic molecules

From: David Mobley (dmobley_at_gmail.com)
Date: Mon Aug 21 2006 - 09:20:42 CDT

If you are interested in looking at the energy landscape for the
interaction between small molecules in solvent, I suggest calculating
potentials of mean force (PMFs) using umbrella sampling or something
similar. Simple evaluation of the pairwise interaction energy between
the molecules won't give you a good idea of the real interactions
since it neglects the effects of solvent entirely (for just one
example, imagine two hard spheres in water -- if you pull them
together, there is a barrier associated with the state where you have
a single water molecule trapped between the two spheres. If you just
evaluate the interaction energy between the two spheres, you can't see
this).

David

On 8/20/06, Björn C-G. Karlsson <bjorn.karlsson_at_hik.se> wrote:
>
>
>
>
> Hi!
>
> I have been using Amber 8 to simulate the interactions between small organic
> molecules in organic solvents such as chloroform and acetonitrile (explicit
> solvent) using NVT and NPT molecular dynamic simulations.
>
> Now my question is: I know that it is possible to extract energy information
> from a simulation such as Etot, Epot and Ektot using a script, but is it
> possible to calculate the non-bonded interactions for single molecules
> during a simulation plotting these values and so to speak get a rough
> measurement on the binding energy when the molecule interacts with another
> molecules and experiences a decrease in Epot?
>
> I have seen that something like this has been published before however using
> the MD software GROMACS (Li, X-Y.; Eriksson, L. A. Molecular Dynamics Study
> of Lignin Constituents in Water (2005). 59, 253-262.) However, can this be
> performed using the Amber 8 software and how do I do it?
>
>
>
> Cheers/Björn
>
>
>
> -----------------------------------------------------------------
>
> Björn C-G. Karlsson
>
> PhD Student in Organic Chemistry
>
> Department of Chemistry and Biomedical Sciences
>
> University of Kalmar
>
> SE-391 82, Kalmar, Sweden
>
> Tel: +46 (0)480-44 62 80
>
> Mobile: +46 (0)70-6150 444
>
> bjorn.karlsson_at_hik.se
>
> -----------------------------------------------------------------
>
>
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