[gmx-users] different PMF results using MPI

[Srinivasa Ramisetti]

Hi,

Thank you Mark. Previously, I did run similar simulations on the same 
number of cores (72 cores) where I noticed small variation in PMF unlike 
the one I am observing now with 36 cores. I can try running few more 
cases to show you the comparison.

Please follow the link for the figure with PMF curves.
https://www.dropbox.com/s/mqaot2olg1hqcj1/pmf-error.png?dl=0

Thank you
Srinivasa
On 22/06/2018 14:57, Mark Abraham wrote:
> 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.
> (The list does not accept attachments - share a link to a file on a sharing
> service if you need to.)
>
> 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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