AMBER Archive (2006)

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

From: David Mobley (dmobley_at_gmail.com)
Date: Thu Aug 24 2006 - 15:07:57 CDT

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
>
>
>
>
>
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu