Re: [AMBER] Total energy of glycan simulation is postive

From: David A Case <>
Date: Fri, 21 Dec 2018 09:00:12 -0500

On Fri, Dec 21, 2018, Rajarshi Roy wrote:
>I simulated a small glycan in an implicit solvent using igb=2. But
>surprisingly the total energy and the potential energy of the system remain
>positive. But the same structure in an explicit solvent is showing negative
>total energy. Can anyone help me out from this? Is it normal to have
>positive energy?

The zero of energy is generally irrelevant in molecular mechanics
calculations, and a positive potential energy is not necessarily a
symptom of a problem.

The explicit solvent calculation includes many favorable (negative)
water-water interactions that are not present in the GB simulation. So
the absolute energy is of little use: concentrate on energy differences.


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Received on Fri Dec 21 2018 - 06:30:03 PST
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