Re: [AMBER] Energy Evaluations

From: Daniel Roe <>
Date: Tue, 5 Jan 2021 11:14:15 -0500


On Mon, Jan 4, 2021 at 11:51 PM Matthew Guberman-Pfeffer
<> wrote:
> I obtain energy values that are different from the original output, as compared below.
> TOTAL VDW ELEC Bond Angle. Dihedral VDW14 elec14
> Origianl MD -569322.9 79197.4 -707668.5 2441.9 6655.1 8500.0 38721.9
> ESANDER -569274.9 79236.1 -707657.7 2446.7 6652.0 8497.8 2829.7 38720.5
> Difference 48.0 38.6 10.8 4.8 -3.1 -2.2 -1.4
> I get the same result as cpptraj if I run sander with imin=5 and ncyc=1. As far as I can tell, the energy value I get from cpptraj are not anywhere in the original MD output, suggesting to me that the values are not simply shifted by some number of frames. Can someone please explain why the energy values are different from the original MD?

So the issue here is that the energies in the MDOUT file are 1 time
step before the coordinates written to the trajectory; i.e. the
coordinates written out are those of the propgated time step (this has
been discussed many times on the mailing list). If you perform a very
short (say 10 step) simulation, writing coordinates and energies every
step, then compare the energies in MDOUT to the ones you get from
post-processing the coordinates (with cpptraj or sander), you'll
notice that the second energy in MDOUT will match the first energy
from post-processing et cetera.

Hope this helps,


> Best,
> Matthew
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Received on Tue Jan 05 2021 - 08:30:02 PST
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