AMBER Archive (2004)

Subject: Re: AMBER: Output of sander

From: David A. Case (case_at_scripps.edu)
Date: Thu Dec 23 2004 - 15:35:49 CST

On Thu, Dec 23, 2004, Harianto wrote:

> I run ANAL program and part of the result is the following:
>
> ----------------------------------------------
> ENERGY CONTRIBUTION BY GROUPS
>
>
> GROUP BOND ANGLE DIHEDRAL VDW14 EEL14 VDWNB EELNB HBOND CONSTRAINT TOTAL
>
> 1 482.64 1547.47 1138.92 404.78 5328.81 -593.00 -9067.62 0.00 0.00 -757.992
> 2 0.00 0.00 0.00 0.00 0.00 552.72 -5515.11 0.00 0.00 -4962.390
> 3 0.00 0.00 0.00 0.00 0.00 11.68 -331.56 0.00 0.00 -319.874
> TOTAL 482.64 1547.47 1138.92 404.78 5328.81 -28.59 -14914.29 0.00 0.00 -6040.256
>
>
> BOND + ANGLE + DIHED INTERACTION ENERGY MATRIX
>
> 1 2 3
> 1 3169.030 0.000 0.000
> 2 0.000 0.000 0.000
> 3 0.000 0.000 0.000
>
> INDIVIDUAL GROUPS INTERACTION
>
> GROUP INTRA INTER TOTAL
>
> 1 3169.03 0.00 3169.03
> 2 0.00 0.00 0.00
> 3 0.00 0.00 0.00
>
> TOTAL 3169.03 0.00 3169.03
>
>
>
> VDW (N-B + 1-4) INTERACTION ENERGY MATRIX
>
> 1 2 3
> 1 -171.699 -43.900 10.859
> 2 -43.900 568.421 12.505
> 3 10.859 12.505 0.000
>
> INDIVIDUAL GROUPS INTERACTION
>
> GROUP INTRA INTER TOTAL
>
> 1 -171.70 -33.04 -204.74
> 2 568.42 -31.40 537.03
> 3 0.00 23.36 23.36
>
> TOTAL 396.72 -20.54 376.19
> -------------------------------------------------
>
> Now, BOND+ANGLE+DIHED interactiion energy matrix is obtained from
> 482.64+167.47+1138.92 = 3169.03, similarly for the other groups.
>
> But for VdW interaction energy matrix (also that of ELECTROSTATIC, not
> displayed) cannot be obtained by the same way, e.g :
> 404.78 -593.0 = -188.22 is not the same as -171.70 in the matrix.
> Similarly for the other groups.
>
> Can you explain it to me, or is there something wrong?
> Thank you very much.

There are two different models being used. The "energy contributions by groups" lists the INTRA +
(1/2) INTER as belonging to the group. So, -171.70 - 33.04/2 = -188.22.
>
> Regards,
> Harianto.
>
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-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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