Re: [AMBER] strategies to speed up MM/GBSA screening

From: Thomas Evangelidis <>
Date: Thu, 14 Jul 2016 01:09:31 +0200

> ​The slow part of the calculation is calculating the forces. Compared to
> that, the cost of integrating positions and velocities is nearly
> negligible. So the question here is "is there any way to efficiently
> calculate only the forces on the atoms you wish to propagate"?
> Unfortunately the answer to that is "no", especially with GB. The
> long-range effect of the nonbonded interactions means you need to compute
> the interactions between all atoms you wish to study (near the active site)
> with all other atoms in the system. And you also can't restrict the
> nonbonded calculation between only the (very small number of) pairs in
> which one atom is one of the "atoms of interest", because the GB potential
> is not pairwise decomposable.
​Which means in simple words that not calculating forces between _fixed
atoms only_ in a GP simulation is wrong?​

> What this means is that the presence (and location) of atom A can influence
> the interaction between atoms B and C (it does this through A's effect on
> the Born radii of both atom B and C). Which means that regardless of which
> atoms you want to integrate, you effectively need to do the whole force
> calculation...
> Moral of the story: If you want to speed up your calculation​, run on GPUs.
> HTH,
> Jason
> --
> Jason M. Swails
> _______________________________________________
> AMBER mailing list

Thomas Evangelidis
Research Specialist
CEITEC - Central European Institute of Technology
Masaryk University
Kamenice 5/A35/1S081,
62500 Brno, Czech Republic

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Received on Wed Jul 13 2016 - 16:30:02 PDT
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