AMBER Archive (2004)

Subject: Re: AMBER: Question concerning ANAL total energy calculation

From: David A. Case (case_at_scripps.edu)
Date: Mon Dec 20 2004 - 16:10:08 CST

On Mon, Dec 20, 2004, Daniel Wetzler wrote:

> I got the following results for sander and ANAL :
>
> from sander :
>
> BOND = 295.8162 ANGLE = 646.4210 DIHED = 1233.8313
> VDWAALS = -2112.7547 EEL = -25900.1470 HBOND = 0.0000
> 1-4 VDW = 833.2051 1-4 EEL = 12661.1189 RESTRAINT = 0.0000
>
>
> and from ANAL :
>
> TOTAL ENERGY = -6657.8538
> NON-BONDED VDW ENERGY = -2248.2623
> NON-BONDED EEL ENERGY = -11164.3808
> HBOND 10-12 ENERGY = 0.0000
> BOND ENERGY = 295.8162
> ANGLE ENERGY = 646.4210
> DIHEDRAL ENERGY = 1233.8313
> NON-BOND 14 VDW ENERGY = 833.2051
> NON-BOND 14 EEL ENERGY = 3745.5157
> BOND CONSTRAINT ENERGY = 0.0000
> ANGLE CONSTRAINT ENERGY = 0.0000
> DIHEDRAL CONSTRAINT ENERGY = 0.0000
> POSITION CONSTRAINT ENERGY = 0.0000
>
> It seems that the main differences are for the calculation of EEL
> enrgies. I don't know how to change the
> ANAL parameters to get nearly the same results.

First, you should use a very large cutoff to make comparisons: anal uses
a residue-based cutoff and sander an atom-based one. These only match in the
limit of no cutoff (which you would want to understand energies anyway).

Second, setting idiel=0 in anal looks wrong: the default behavior in sander
is for a constant dielectric model, so you should use the same thing (idiel=1,
I believe) in anal.

...dac

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