Re: [AMBER] Implicit solvent simulation with Andersen thermostat

From: Glenn Carrington [bs10g3c] <>
Date: Fri, 27 Mar 2015 11:31:17 +0000


Thanks very much for the feedback and to Jason for the input files. Some useful pointers there.
I think there has been a misuderstanding though, in that the x2 speedup on the GPU is Berendsen versus Langeivein. Not Anderson.
I will try again with the new settings and get a better idea of timings over the next couple of weeks. Thanks again for your help!

Many thanks,

> On 26 Mar 2015, at 16:33, David A Case <> wrote:
> On Thu, Mar 26, 2015, Glenn Carrington [bs10g3c] wrote:
>> I initially used the Langevin thermostat as per the AMBER tutorial, but
>> it took ages to get 100 steps on the GPU. Switched to Berendsen and
>> the GPU simulation ran noticeably faster. I have not got the timings
>> to hand, but I'm guessing a x2 speed increase at least. However,
>> as mentioned I don't think I can use this thermostat with implicit
>> solvent. As the structure has 47,000 atoms, do you think the difference
>> between Anderson and Langevin will be more pronounced due to the
>> system size? I'm hoping so, as the simulation will be painfully slow
>> otherwise.
> Be sure to look at the benchmarks shown on the Amber web page. The nucleosome
> GPU values (closest to yours) are for 25,000 atoms. Doubling the number of
> atoms is likely to increase execution time by a factor of 4, and you should
> see if your timings are in rough agreement with that estimate. It is
> certainly true that Amber's GPU implementation of GB is not optimal for large
> numbers of atoms.
> I think the Anderson thermostat should be fine for GB, but I have not ever
> used it that way. But my GB runs are usually on much smaller systems.
> ....dac
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Received on Fri Mar 27 2015 - 05:00:03 PDT
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