AMBER Archive (2006)

Subject: Re: AMBER: md and implicit solvation

From: Thomas Cheatham (
Date: Tue Oct 24 2006 - 20:50:43 CDT

> I ran 50 ps of an MD simulation (equilibration phase) using implicit
> solvation. However my calculation took 3 days to complete! Is it normal to
> take so long? I am really worried because I want to run a production phase of
> 1 ns. I wonder if someone could tell me if there is something wrong with my
> script or pehaps suggest me modifications to improve it. My system has around
> 15000 atoms.

The key here is probably that you are simulating a system of 15,000 atoms
in the gas phase (with continuum solvent)... This is on the order of
~1500 amino acids. Despite specifying a cutoff, the generalized Born
simulations in Amber do not have a pairlist and effectively look over all
pair interactions (although you can set RGBMAX to a lower value to perhaps
increase speed a little). To date, the implicit solvent code has not been
optimized for large systems. In this case, you may actually be better off
running with particle mesh Ewald and explicit solvent (as you saw)!


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