Hi Guanglin,
Yes, your simulations using Amber 16.05 are incorrect - the 12-6-4 potentials would have been ignored and so the results are not reliable and should be published. The 12-6-4 potential has never been supported by the GPU code and still isn't. It was the responsibility of the person who added 12-6-4 support to pmemd to also add traps to make sure other parts of code that did not support their potential would quit if one tried to use it. Unfortunately they did not do that, nor was there a warning added to the tutorial that GPU support was not present and so unfortunately a number of people will have unwittingly run simulations believing they were using the 12-6-4 parameters. The trap was added in the latest update when the omission was spotted.
Such failures should serve as a warning to anyone adding features to scientific codes where they are not writing comprehensive support - you run the risk of wasting lots of people's time and, in some cases causing people to have to retract papers. It is firmly the responsibility of the person adding the new methodology to properly deal with this.
In terms of running the 12-6-4 potentials with the GPU code this requires someone to write, test, optimize and validate the code to support this. I have brought this up multiple times but nobody seems to want to volunteer to do it. As such at present the 12-6-4 potential is only available in the CPU code, and in my opinion this should be made clear in anything that references the 12-6-4 potential until such a time that it is supported.
I would also note that any papers published that used the 12-6-4 potential and relied on the PMEMD GPU code should be retracted.
All the best
Ross
> On Jan 11, 2018, at 22:01, Guanglin Kuang <guanglin.kth.se> wrote:
>
> Hi David,
>
> I'm afraid I don't fully get your points.
>
> When I follow the instructions on "http://ambermd.org/tutorials/advanced/tutorial20/12_6_4.htm", the same simulation can run on Amber 16.05, but it failed on Amber 16.12.
>
> If 12-6-4 potentials are not supported in the CUDA code, are the results produced by Amber 16.05 with CUDA GPU for a system containing these potentials problematic and not reasonable at all? If not, how can we make it run on Amber 16.12?
>
> Thanks!
> Best regards,
> Guanglin
>
>
> ________________________________________
> From: David Cerutti <dscerutti.gmail.com>
> Sent: Friday, January 12, 2018 6:11 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Amber 16.12 and 12-6-4 force field Problem
>
> We've just had another discussion about this problem. The problem is that
> there was never any support for 12-6-4 potentials in the CUDA code, so you
> haven't lost any functionality. The bug was that the code was still
> allowing you to run topologies containing those parameters without actually
> changing the potential at all, so you might have thought that they were
> part of the simulation even though they weren't.
>
> On Thu, Jan 11, 2018 at 9:49 PM, Guanglin Kuang <guanglin.kth.se> wrote:
>
>> ?
>>
>> Dear Amber Users,
>>
>>
>> I just updated Amber 16.05 and AmberTools 16.13 to the latest Amber 16.12
>> and AmberTools 17.08.
>>
>>
>> Now the 12-6-4 force field parameters for ions seem to be not supported in
>> Amber 16.12, with the following error in the output file:
>>
>> CUDA (GPU): Implementation does not support 12-6-4 LJ potential.
>> The topology contains 12-6-4 coefficients and must be changed.
>>
>> Input errors occurred. Terminating execution.
>>
>> Anyone encounter this problem and any solutions?
>>
>> Thank you!
>> Best regards,
>> Guanglin?
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Sat Jan 13 2018 - 12:30:02 PST
