Re: [AMBER] Fwd: Implicit solvent GB calculation

From: Daniel Roe <>
Date: Mon, 7 Mar 2011 10:40:34 -0500


You are running GB with an extremely large cutoff (300.0 Ang) so I
think that 1.3 ns/day is not unreasonable for ~7600 atoms.

Also note that your specific system setup (CPU, interconnect speed,
compilers used etc) will impact your timing. You can run the
benchmarks included with Amber and compare to existing benchmarks
( to get an idea for how your system
measures up.


On Mon, Mar 7, 2011 at 10:04 AM, Rubben Torella
<> wrote:
> Dear Amber community,
> I'm trying to perform MD simulation in implicit solvent using Generalized
> Born approach on a protein-DNA complex.
> I followed the tutorial described here (
> order to set-up the calculation.
> We are talking about 7637 atoms in the complex.
> I launched the calculation on 64 processors (10 ns), but the calculation
> seems to me very slow (1.3 ns/day)
> Is there something wrong in this approach or is it normal to have this
> calculation speed?
> I attached you the input of the MD calculation, in order to know if there
> are mistakes or there is some flags that slow down the calculation.
> Thank you for your help
> Rubben
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Received on Mon Mar 07 2011 - 08:00:04 PST
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