Re: [AMBER] time of MD

From: Jacopo Sgrignani <>
Date: Mon, 24 Oct 2016 10:47:21 +0200

Dear Stefania
are you running in explicit or implicit solvent?
In the first case the incredible increasing of the simulation time could be
due to the use of a larger water box.
You should control the total number of atoms you have in the two systems
and pay attention to the box size.

Which machine are you using for the simulation?



2016-10-24 10:33 GMT+02:00 Stefania Mirabella <>:

> Hello,
> 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!
> I am using the gaff force field for the organic ligand.
> There is something I can do to obtain a reasonable time or I have to
> give up with this ligand?
> Thank you
> Stefania
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Received on Mon Oct 24 2016 - 02:00:03 PDT
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