[gmx-users] changing cutoffs with gmx tune_pme

[Mark Abraham]

Hi,

On Mon, 24 Jul 2017 14:48 Leandro Bortot <leandro.obt at gmail.com> wrote:

> Dear users,
>
>      I'm doing some tests with gmx tune_pme to optimize the setup for my
> system. In the help options I saw that I could change the coulomb and LJ
> cut-offs in addition to varying the number of PME ranks. So I did that to
> test.
>

Shameless plug for background discussion...
http://onlinelibrary.wiley.com/enhanced/exportCitation/doi/10.1002/jcc.21773

     My system runs faster when rcoulomb and rvdw are small. Specifically =
> 0.5 nm in my tests.
>

Don't. rvdw is not a free parameter - most forcefields won't work if you
change it. You would likely have better prospects if you also used
dispersion PME in recent versions of GROMACS, but the field lacks
experience with that yet.

Mark


     When I compare test runs for the same number of PME ranks I see that
> fourier-nx, fourier-ny and fourier-nz change with the cut-off, but
> fourierspacing remains constant.
>
>      My question is: is actually running the production run with such small
> cutoffs justifiable?
>      I think it is not and that this would break the forcefield (AMBER99).
> I would like to hear what you think about that.
>
>
>      Here is some data in case it is helpful:
>
> For the same number of cores and PME ranks:
>
> Performance = 4.688 ns/day
>    rcoulomb                       = 1
>    rvdw                               = 1
>    fourierspacing                = 0.12
>    fourier-nx                     = 320
>    fourier-ny                     = 120
>    fourier-nz                     = 120
>    pme-order                      = 4
>    ewald-rtol                     = 1e-05
>    ewald-rtol-lj                  = 0.001
>
> Performance = 2.060 ns/day
>    rcoulomb                       = 1.5
>    rvdw                              = 1.5
>    fourierspacing                 = 0.12
>    fourier-nx                     = 208
>    fourier-ny                     = 80
>    fourier-nz                     = 80
>    pme-order                      = 4
>    ewald-rtol                     = 1e-05
>    ewald-rtol-lj                  = 0.001
>
> Performance = 8.248 ns/day
>    rcoulomb                       = 0.5
>    rvdw                           = 0.5
>   fourierspacing                 = 0.12
>    fourier-nx                     = 640
>    fourier-ny                     = 240
>    fourier-nz                     = 240
>    pme-order                      = 4
>    ewald-rtol                     = 1e-05
>    ewald-rtol-lj                  = 0.001
>
>
> Best regards,
> Leandro
> --
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