Re: [AMBER] Difference of internal energy

From: Jason Swails <>
Date: Mon, 22 Nov 2010 09:33:41 -0500

I'm not exactly sure what you're asking, or what you're saying your result
is, but I'll try my best to explain based on how I interpreted your email.

If you're using a multiple trajectory approach, then it's perfectly
reasonable to be getting a change in the internal energy upon binding.
However, if you're using a single trajectory approach, then all internal
potential terms should exactly cancel, since the internal coordinates of all
bonded interactions remain exactly the same. I would be OK with slight
variations based on round-off error when converting cartesian coordinates to
internal coordinates, but 318.2 kcal/mol is too large in this instance.

Hope this helps,

On Mon, Nov 22, 2010 at 9:06 AM, Kshatresh Dutta Dubey

> Dear All,
> I am calculating binding energy between two chains of a dimer using MM-PBSA
> method. I considered one chain as ligand and other as receptor. I got
> difference of internal energy as 318.2 Kcal/mol. However, it comes zero in
> most cases. Is this result correct ? If yes, then what is its significance?
> Please give me some idea about this output.
> Thanks in advance
> Kshatresh
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Mon Nov 22 2010 - 07:00:03 PST
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