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Re: [lammps-users] Question about using r-respa integrator
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Re: [lammps-users] Question about using r-respa integrator


From: Pengyu Huang <hughh.py@...24...>
Date: Thu, 12 Apr 2018 14:13:05 +1000

Thanks for reminding me, Axel. I forgot to click the 'Reply to all'. I am posting what I wrote in the previous email last night:


On Thu, Apr 12, 2018 at 4:34 AM, Axel Kohlmeyer <akohlmey@...43...4...> wrote:
please always reply to the mailing list and not only individual
people. thanks, axel.

On Wed, Apr 11, 2018 at 1:40 PM, Pengyu Huang <hughh.py@...24...> wrote:
> Thank you very much, Axel, for your suggestions.
>
> I thought by defaults the bond, angle, dihedral and improper forces are
> calculated at the innermost timestep, and the multi-cut off setups are for
> the pair forces calculation, as the documents says " If not specified, the
> defaults are that bond forces are computed at level 1 (innermost loop),
> angle forces are computed where bond forces are, dihedral forces are
> computed where angle forces are, improper forces are computed where dihedral
> forces are, pair forces are computed at the outermost level, and kspace
> forces are computed where pair forces are.  " Thanks for pointing out this,
> I will double check the setup.
>
> Also thanks for your suggestions for the co2. I also want to model co2 with
> flexible bonds and angle, so in this case I do not need a rigid integrator
> and using r-RESPA might help?
>
> Regards,
> Pengyu
>
> On Thu, Apr 12, 2018 at 3:11 AM, Axel Kohlmeyer <akohlmey@...24...> wrote:
>>
>> On Wed, Apr 11, 2018 at 1:04 PM, Pengyu Huang <hughh.py@...24...> wrote:
>> > Dear all,
>> >
>> > I would like to model flexible water, co2 and solid surfaces in my
>> > system
>> > with LAMMPS, which requires a very small time step (for flexible water),
>> > i.e. dt = 0.25 fs. I think r-respa may be one way to speed up the
>> > simulation. According to the LAMMPS document, it suggests using the
>> > following setup, so that the innermost time step is 0.5 fs:
>> >
>> > timestep  4.0
>> > run_style respa 4 2 2 2 inner 2 4.5 6.0 middle 3 8.0 10.0 outer 4
>> >
>> > I will try this set up in my simulations with timestep = 2 fs so that
>> > the
>> > innermost timestep is 0.25 fs (for bonds and angles) . My question is:
>> > apart
>> > from checking the energy conservation, is there any "pitfalls" about
>> > using
>> > the r-respa method in molecular dynamics simulations that I should pay
>> > attention to? It will be great if anyone who has had experiences with
>> > the
>> > r-respa method can provide any comments, suggestions or hints. All
>> > comments
>> > are welcome.
>>
>> you are confusing multi-cutoff separation with bond/angle/pair separation.
>> you are not going to save much time with your setup from above, since
>> you are computing a lot of interactions multiple times.
>>
>> you probably want something like this:
>>
>> timestep 4.0
>>
>> run_style respa 3 4 2 dihedral 1 pair 2 kspace 3
>>
>> however, the biggest problem is not the flexible water, but the co2.
>> for that you would need a rigid integrator and those will require a
>> short time step anyway to run stable.
>> so using r-RESPA may not be as helpful as you expect.
>>
>> axel.
>>
>>
>> >
>> > Thank you for your time.
>> >
>> > Regards,
>> > Pengyu
>> >
>> >
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>> >
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
>> College of Science & Technology, Temple University, Philadelphia PA, USA
>> International Centre for Theoretical Physics, Trieste. Italy.
>
>



--
Dr. Axel Kohlmeyer  akohlmey@...43...4...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.



Regards,
Pengyu