see below
On Wed, Jul 13, 2016 at 7:09 PM, Thomas Evangelidis <tevang3.gmail.com>
wrote:
> > 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?
>
> yes, because it isn't really just about the forces. the issue is that in
> order to calculate the interaction/force between a moving atom and a fixed
> atom, you need to have the effective Born radii of both atoms, but
> calculating the effective radii of the fixed atoms requires calculating
> their distance to all other atoms. As Jason said, it isn't pairwise
> decomposable, and the need to do 2 steps means that even if you skip some
> interactions in the interaction calculation you don't gain too much since
> you still calculate the N^2 distances for the effective radii. You could
> possibly save effort by doing the radii less frequently (supported in the
> code), but you'd need to program in skipping some of the direct
> interactions since that is currently not done in the GB force routine.
>
> > 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
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
>
> ======================================================================
>
> Thomas Evangelidis
>
> Research Specialist
> CEITEC - Central European Institute of Technology
> Masaryk University
> Kamenice 5/A35/1S081,
> 62500 Brno, Czech Republic
>
> email: tevang.pharm.uoa.gr
>
> tevang3.gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Wed Jul 13 2016 - 18:30:04 PDT
