[gmx-users] different PMF results using MPI

[Mark Abraham]

Hi,

What range of variations do you see in replicates run on the same number of
cores? Maybe you've just observed that your sampling is not yet sufficient.
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Mark

On Fri, Jun 22, 2018, 15:46 Srinivasa Ramisetti <S.B.Ramisetti at leeds.ac.uk>
wrote:

> Dear GMX-USERS,
>
>
> I have a doubt trusting the PMF curve of a single molecule pulled from an
> immobile calcite surface using pull code with umbrella sampling in GROMACS.
> I extracted two PMF’s for the same system (all inputs are the same) by
> running simulations on 36 and 72 cores with MPI to check the consistency of
> the results. I find a significant change in the magnitude of the two curves
> (please see attached the image). The figure also shows the error of PMF
> obtained using bootstrap method. The histogram for both the cases are well
> overlapped.
>
>
> Is it okay to rely on this results? Can anyone suggest how I can reproduce
> similar PMF results by running simulations on any number of cores?
>
>
> These results were produced using gromacs 2016.4 version with the
> following pull code:
>
>
> pull = yes
>
> pull_ngroups = 2
>
> pull_ncoords = 1
>
> pull_group1_name = SUR ; calcite surface
>
> pull_group2_name = MDX ; organic compound
>
> pull_coord1_type = umbrella ; harmonic biasing force
>
> pull_coord1_geometry = distance ; simple distance increase
>
> pull_coord1_groups = 1 2
>
> pull_coord1_dim = N N Y
>
> pull_coord1_k = 500 ; kJ mol^-1 nm^-2
>
> pull_coord1_rate = 0.0
>
> pull_coord1_init = XXX ; XXX is the COM distance between 2 groups
>
> pull_coord1_start = no
>
>
> Thank you,
>
> Srinivasa
>
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