Re: [AMBER] Electrostatic energy in a simple non-periodic system

From: David A Case <>
Date: Wed, 17 Nov 2021 09:20:03 -0500

On Wed, Nov 17, 2021, Ali Morshedi wrote:
>I put two ions (one Na+ and one Cl-) at a distance of r=4.15 angstroms.
>I expect the coulombic energy to simply be k_e q1*q2/r =
>18.2223^2*1*1/=80.01 kcal/mol.
>However, a minimization with zeros steps (which I expect should give the
>energy of initial configuration) is giving me "EEL = -3.2695".
>I'd appreciate it if you let me know what I'm doing wrong and why I'm
>getting the discrepancy.
>Please find attached relevant files for the example.

You made a periodic system, with a box around your ions. Then you set ntb=0
in the input file. I'm not sure that ntb cancels all effects of the box.
See if setting up a non-periodic system helps.

Or, you could set igb=6: that will give a non-periodic calculation
even if the prmtop file has box information in it. Simply adding igb=6
gives me an EEL of -80 kcal/mol.


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Received on Wed Nov 17 2021 - 06:30:02 PST
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