Thanks Ross. I am planning on transfering the sander based angle/torsion
COM restraints to pmemd but this will probably start after September 2016.
I will let you know about the progress so that we can make sure it will
work in pmemd.CUDA, too.
All the best,
Ilyas Yildirim, Ph.D.
-----------------------------------------------------------
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On Thu, 26 May 2016, Ross Walker wrote:
> Hi Ilyas,
>
> I haven't had a chance to look properly unfortunately. If the CPU code in PMEMD properly supports angle and dihedral restraints for center of mass (I'm pretty sure it does but have never actually tried it) then it might be possible to hack in GPU support in the GPU download / GPU upload fashion - that would get it working at least although probably a 50% performance hit - it could be mitigated perhaps by only downloading the atoms involved in the COM groups but if they are > say 10% of the total atom count it probably wouldn't make a difference. One could then look to write GPU kernels for the angle and dihedral COM restraints. I just wish the restraint code wasn't such a mess from the early 90s - it would be way easier if it was clearer.
>
> The distance based COM stuff was funded under work on looking at lipid diffusion which didn't need angle or dihedral hence why it was never implemented. If anyone has someone who might be able to do it I'd be happy to work with them on getting it implemented.
>
> All the best
> Ross
>
>> On May 26, 2016, at 10:01 AM, Ilyas Yildirim <iy222.cam.ac.uk> wrote:
>>
>> Ross, does the pmemd code need to be changed so that angular and torsional COM restraints can be used with pmemd.CUDA or any file under $AMBERHOME/src/pmemd/src/cuda requires modification, too?
>>
>> Ilyas Yildirim, Ph.D.
>> -----------------------------------------------------------
>> = Website: http://ilyasyildirim.wordpress.com =
>> = ------------------------------------------------------- =
>> = http://www.linkedin.com/in/yildirimilyas =
>> = http://scholar.google.com/citations?user=O6RQCcwAAAAJ =
>> -----------------------------------------------------------
>>
>>
>> On Thu, 26 May 2016, Ross Walker wrote:
>>
>>> If grant funding becomes available to support me doing this then yes. Otherwise no.
>>>
>>>> On May 26, 2016, at 5:50 AM, Åsmund Røhr Kjendseth <asmund.rohr.nmbu.no> wrote:
>>>> Dear Amber developers,
>>>> in the Amber16 advertisement it was stated “Enhanced NMR restraint support” for the GPU version. I have been looking forward to use COMs for angel and dihedral restraints, however, this seems not to be supported yet:
>>>> CUDA (GPU): Implementation does not currently support the use of COM simulations for angle or dihedral restraints.
>>>> Require iat(3) >= 0.
>>>> Could you please indicate whether this is prioritised in future updates or not?
>>>> Best regards,
>>>> Aasmund Kjendseth
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Received on Fri May 27 2016 - 06:30:03 PDT
