[gmx-users] cutoff-sch​eme in CPU& GPU

[Szilárd Páll]

Most probably this has nothing to do with the cut-off scheme. Please
read this page:
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
--
Szilárd


On Wed, Jul 16, 2014 at 8:44 PM, leila salimi <leilasalimi at gmail.com> wrote:
> Dear GROMACS Users,
>
> I have a question regarding the Neighbor searching, I used group scheme
> when I used 4.5 and now I found that there is verlet in version 4.6. When I
> compare the trajectories, For verlet simulation I found that the atoms of
> water molecules are separated and it caused the long bond in vmd. I mean
> that one hydrogen is located on the right side of the cell and the oxygen
> and another hydrgon are on the left side that the first hydrogen can come
> with periodic image, but these long bond (artifact bonds) are not
> convenient and it is difficult for visualization.
>
> I did not have this problem with previous method (group). Could you explain
> me what it is happened in  Cut-off schemes = verlet?
> And is it possible to have the trajectory with the right bonds (not broken
> bond)?
>
> Kind Regards,
>
>
> On Sun, May 25, 2014 at 5:39 PM, Szilárd Páll <pall.szilard at gmail.com>
> wrote:
>
>> On Sat, May 24, 2014 at 9:39 PM, Que Pasa <quepasa41 at gmail.com> wrote:
>> > Yes. You can. The entire program was built and was functional on CPUs
>> well
>> > before GPUs came into the picture. Due to the way calculations are
>> > off-loaded to GPUs not all features available on CPUs are available in
>> the
>> > GPU implementation. "cutoff-scheme = Verlet" is one such example. For
>> more
>>
>> I guess you meant "cutoff-scheme = Group". The Verlet scheme is the
>> one that supports GPU acceleration while the (traditionally default up
>> until v5.0) Group scheme does not.
>>
>> Also note that in 5.0 nearly all features will be supported in the
>> Verlet scheme!
>>
>> --
>> Szilárd
>>
>> > details please read http://www.gromacs.org/GPU_acceleration and the
>> > relevant papers.
>> >
>> > hth
>> >
>> >
>> > On Sat, May 24, 2014 at 3:52 AM, Yorquant Wang <wangykoo at gmail.com>
>> wrote:
>> >
>> >> Hi, all
>> >>
>> >>     Recelly I am testing the speed of GMX4.6 on our new supercomputer.
>> >> There are two parameters "cutoff-scheme " and "nstlist ".
>> >>        for GPUs I uesd:
>> >>            cutoff-scheme=Verlet
>> >>            nstlist                  = 20
>> >>        I found the speed is fast.
>> >>
>> >>   I have tested if I use "cutoff-scheme=Verlet" combined with
>> >> "nstlist=20" for CPUs, the speed was pretty fast. Could I use the same
>> >> parameter for CPUs?
>> >>
>> >> --
>> >> Yukun Wang
>> >> PhD candidate
>> >> Institute of Natural Sciences && College of Life Science, Shanghai Jiao
>> >> Tong University
>> >> Cell phone: 13621806236.
>> >> China Shanghai
>> >> --
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