Re: [AMBER] time of MD

From: David A Case <>
Date: Mon, 24 Oct 2016 07:58:53 -0400

On Mon, Oct 24, 2016, Stefania Mirabella wrote:

> I am running MDs with Amber of ligand-protein complexes of 20 ns. When
> I used a small ligand (MW about 300 Da) the dynamic was long 3-4 days,
> but when I changed to a ligand three times bigger (around 900 Da) the
> time is dramatically increased to 330 days!

Something seems quite wrong. Amber MD programs print out timings details at
the end of each run...look at those to see if you can see what is different
between the two runs.

MD times are generally, and roughly, linear in the number of atoms being
simulated. Since your protein is probably(?) much bigger than you ligand, the
two simulations should take about the same amount of time.

As you can appreciate, no one will be able to provide more specific
information based on the single sentence description provided above.


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Received on Mon Oct 24 2016 - 05:00:02 PDT
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