Hi all,
has anyone had any experience with amber.cuda using Nvidia S2050
rack-mounted units? I wonder if there is any loss in performance due to
each pair of Tesla cards sharing a PCI-E slot on the motherboard.
It didn't seem to be a problem with the previous generation cards, but
with faster Fermi cards the bottleneck could possibly shift to the
interface. Has anyone seen such a drop in individual performance when
all cards in S2050 execute at the same time?
Thanks for any info
Sasha
Ross Walker wrote:
> Hi Dean,
>
>
>> I have a quick question:
>>
>> I'm just curious as to the theoretical explanation for why the box
>> clearance
>> should be greater than your cutoff?
>>
>
> The requirement, due to the fact that AMBER implements the minimum image
> convention within the code. In that it does not have image atoms and expects
> each atom to only interact with itself once in the direct space calculation
> means that the minimum box dimension must be at least the cutoff size.
>
>
>> If I did 10A clearance for my protein in a water box, and used 10A for
>> my cutoff, what would be the deleterious results?
>>
>
> In this case your box is almost certainly large enough even allowing for the
> density increasing during NPT runs. The solvatebox command in leap adds
> sufficient water so that no single solute atom is within the buffer distance
> of the box edge. In your case if your protein was 10 angstroms by 10
> angstroms by 10 angstroms (pretty small!) then you would have added a
> minimum of 10 angstroms of water on each side of your solute. This gives you
> a box with a minimum size of 30 angstroms^3. This is 3 times larger than the
> minimum size implied by the minimum image convention with a 10 angstrom
> cutoff so you have significant room to spare.
>
> Note, the code continually checks that the minimum image convention is not
> violated and will quit it your box becomes too small rather than running and
> generating incorrect answers.
>
> I hope this helps.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
>
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>
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Received on Mon Jun 07 2010 - 09:30:03 PDT
