Re: [AMBER] Inconsistent Internal energy from monomer to dimer

From: Josep Maria Campanera Alsina <>
Date: Thu, 5 Apr 2012 13:11:13 +0200

I rewrite my previous email clearer.

.The internal energy (BOND+ANGLES+DIHED) for the dimer (AB) was
computed 1136 kcal/mol.
-The internal energy of the splitted monomers (A and B that come from
the AB dimer) was slightly different between both monomers but around
the value of 567-568 kcal/mol. Lets say 569 kcal/mol for one and 567
kcal/mol for the other one. I do not have the exact values with me now
but they weren't much different. These values are consistent with the
AB value.
-The internal energy for the free monomer was computed to be 545
kcal/mol. This value doesn't match with the dimer AB value of Internal

All comments are welcome. I've attached the output files for
inspection in previous emails.

All the best,

Josep M.,

Message: 16
Date: Wed, 4 Apr 2012 05:37:37 -0400
From: Carlos Simmerling <>
Subject: Re: [AMBER] Inconsistent Internal energy from monomer to
To: AMBER Mailing List <>
Content-Type: text/plain; charset=ISO-8859-1

i'm not sure i understand your statements here, and I want to make sure its
you calculated 3 trajectory energies- the dimer trajectory (AB), and then
each of the 2 monomers from the same trajectory (A+B). You're saying that
A+B still isn't equal to AB. I'm asking because below you only quote 2
energies, and I'm not sure if you mean to say that the split monomers had
identical energies (possible, but seems unlikely).
If this is the case, then something is clearly wrong with the energy
calculations (or perhaps in the inputs).
Can you confirm, and provide all 3 energy values?

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Received on Thu Apr 05 2012 - 04:30:04 PDT
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