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

From: Carlos Simmerling <>
Date: Tue, 3 Apr 2012 07:25:32 -0400

in order to check the code, I think the right way to go is to use ptraj to
split the dimer trajectory into 2 monomer trajectories. then the
conformations are the same, so the energies should match. I can completely
expect that the dimer trajectory has different structure than the monomer,
and so the dihedral energies are different. perhaps the dimer optimizes
nonbonded interactions, and in the monomer the dihedrals can relax wityhout
the nonbonded constraints.

On Tue, Apr 3, 2012 at 7:15 AM, Josep Maria Campanera Alsina <> wrote:

> Dear all,
> I have found an inconsistency in MMGBSA/PBSA calculations that
> embittering me. This is about the internal INT term (BOND+ ANGLES
> +DIHEDRALS) in the MMGSBA decomposition only. A colleague has passed
> to me two simulations run apparently under the same conditions in
> AMBER11. One simulation consists of a peptide of 26 residues (408
> atoms) and the other one a dimer of the SAME peptide with 52 residues
> (816 atoms), the double of the same atoms. I've run the MMGBSA
> analysis (AMBER11 perl and python scripts) and the INT term
> (BOND+ANGLE+DIHED) of the DIMER (1135.89 kcal/mol) is not, by far, the
> double of the INT term of the MONOMER (545.67 kcal/mol). I would just
> expect approximately a double value. Actually, there is a difference
> of 22 kcal/mol (1135.89/2-545.67)!!!!!!!!
> Here is my question, How can be that the internal energy per monomer
> unit changes so much? I think it cannot be! BOND, ANGLES AND DIHED
> cannot be so different in both systems, actually should be very
> similar in terms of monomer units. I've been trying a lot of things
> (topology files, amber inputs etc.) to correct this but I haven't
> found anything strange, neither in the dynamics nor in the MMGBSA!
> What do you think? Is this energy values normal? What's wrong here?
> Where should I focus?
> All comments will be welcome.
> Josep M.,
> PD: Find attached amber files for inspection.
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Received on Tue Apr 03 2012 - 04:30:05 PDT
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