AMBER Archive (2006)

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

From: David LeBard (david.lebard_at_asu.edu)
Date: Thu Aug 24 2006 - 16:01:16 CDT

What about using the radial distribution function(s) to calculate the
potential of mean force between two atoms on opposing molecules?

Just a thought,
David LeBard

On Thu, 2006-08-24 at 13:07, David Mobley wrote:
> Bjorn,
>
> I don't know if it can be done in AMBER; perhaps someone else can
> comment on that.
>
> However, I am still not sure the question you are asking is entirely
> well posed. You might want to think carefully about what you hope to
> get from this. You need a metric to define what "interacts" means, and
> even given that, it is not entirely clear to me what you can get from
> it. I guess you could say that the difference in the
> bupivacaine-environment interaction potential energy is [some number]
> between when it is "interacting" with MAA and when it is not. If
> that's what you want, that's fine, it's just not clear to me how it is
> physically meaningful.
>
> David
>
> On 8/23/06, Björn C-G. Karlsson <bjorn.karlsson_at_hik.se> wrote:
> >
> >
> >
> >
> > Hi David!
> >
> > Thank you for your quick reply!
> >
> > However, by reading your suggestion I realise that I may have been a little
> > bit vague...
> >
> >
> >
> > In my simulations I want to investigate how two different (or the same)
> > molecules interact in explicit chloroform or acetonitrile.
> >
> >
> >
> > Typically, my simulations are comprised of 6 molecules of bupivacaine (a
> > local anaesthetic drug) and 74 molecules of methacrylic acid and
> > approximately 500 molecules of either chloroform or acetonitrile at NPT and
> > NVT.
> >
> > It would be nice if there exist some method or way to extract the energy
> > components of one of these molecules during a MD simulation so that it is
> > possible to e.g. follow how the potential energy drops for one molecule of
> > bupivacaine (in the mixture) drops when that molecule interacts with one (or
> > several) molecules of MAA?
> >
> >
> >
> > As I described in my previous message I have seen something like this
> > published before involving the interaction between two lignin constituents
> > in water using GROMACS but can it be done with AMBER and if so how?
> >
> >
> >
> > I hope that I have made things a little bit clearer
> >
> >
> >
> > Cheers/Björn
> >
> >
> >
> >
> >
> >
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