Re: [AMBER] Implicit solvent simulation is unexpectedly slow

From: 浅井 賢 <>
Date: Sun, 02 Aug 2015 22:59:57 +0900

Dear David,

Thanks for the reply :-)

I see, yeah I wondered that case but I was not really sure so your
explanation helped me a lot.
I didn't really even know the benchmark page has that much examples,
that helps me a lot as well :-)

Thanks again for your help!


On 08/02/2015 09:30 PM, David A Case wrote:
> On Sun, Aug 02, 2015, 浅井 賢 wrote:
>> Several years ago, I performed a simulation with explicit solvent model,
>> Recently, I performed a similar simulation with implicit solvent model,
> You can't expect to compare the timings of these two sorts of simulation
> models in any obvious fashion. The cuda implementation of GB does not
> provide for cutoffs, so you are explicitly evaluating all pair interactions.
> By contrast, explicit solvent simulations use PME to handle long-range
> interactions.
> The Amber GPU benchmark page has lots of good data. It shows that a
> 25,000 atom system with GB runs at something like 7 ns/day on two very
> recent GPUs. This doesn't sound all that different from what you report.
> That page also shows a 90,000 atom explicit solvent system that runs at
> 50ns/day, for comparison. Explicit solvent calculations are often much faster
> than the correpsonding implicit ones.
> If you are worried about the settings you are using, compare them to those
> given the benchmark page.
> ....hope this helps....dac
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Received on Sun Aug 02 2015 - 07:30:02 PDT
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