AMBER: md potential energy

From: Francesco Pietra <>
Date: Mon, 23 Jul 2007 09:14:48 -0700 (PDT)

With a non polymeric large new molecule (parameters from antechamber/gaff) I
run (Amber9) a simple GB MD in analogy with 4.2 of tutorial B1 (igb=1 standard,
ie water).

The molecule represents the less strained conformer obtained from a
global-space conformational search with a molecular mechanics package (MM3-like
force field in vacuum). I.e., I am using a "discrete conformational sampling"
approach, though I hope also to find later the way to a suitable simulated
annealing with Amber9.

The potential energy soon becomes stable, just as in the xmgrace plot of at
4.3 of tutorial B1. Though, it starts at ca +30, attaining constancy at ca

What these positive values of the potential energy mean? Examination of the
mdcr file with VMD shows the molecule grossly in order. Nothing grossly wrong
occurred. I have not calculated rms.

Although all that is encouraging (final task: interaction with receptors), I am
worried by the positive values.


francesco pietra

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Received on Wed Jul 25 2007 - 06:07:20 PDT
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