AMBER: Calculate interaction energy between small organic molecules

From: Björn C-G. Karlsson <>
Date: Thu, 24 Aug 2006 08:17:56 +0200

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

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






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Received on Sun Aug 27 2006 - 06:07:10 PDT
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