[Openchemistry-developers] GSoC '16 Proposal

[Anish Pednekar]

Thank you for your feedback! I have submitted the project proposal through
the GSoC application website. Looking forward to working with the
OpenChemistry team! In the meantime, is there anything I could do? I am
going through the OpenBabel code and familiarizing myself with the code and
style. I am also trying to familiarize myself with the chemistry as I have
no background in it.

Thanks,
-Anish

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On Fri, Mar 25, 2016 at 7:18 AM, Geoffrey Hutchison <
geoff.hutchison at gmail.com> wrote:

> No. We want your choice as to what you think is the best approach. (We
> don't know - that's why it's a GSoC project - it's not clear what the best
> approach is.)
>
> Hope that helps,
> -Geoff
>
> Thank you for your response. I have gone through the links and I would
> like to ask if we are expected to do both i.e adapting OpenMM for other
> molecular fields as well as writing a new implementation for the existing
> OpenBabel code to speed up the calculations using OpenMP/OpenCL?
>
> On Wed, Mar 23, 2016 at 9:31 PM, Geoffrey Hutchison <
> geoff.hutchison at gmail.com> wrote:
>
>> > Hi, I am Anish Pednekar, a second year student studying Information
>> Technology at Goa College of Engineering, India. I'd like to contribute to
>> openchemistry through Google Summer of Code. I have gone through the GSoC
>> ideas page and the project - GPU and Multi-Core Enabled High Performance
>> Force Field Calculations interested me.
>> >
>> > I have worked with Cuda and OpenCL before and have successfully
>> completed courses on Udacity and Coursera. I served as a community TA for
>> the Heterogenous Parallel Programming course on Coursera. I am also
>> familiar with Git.
>>
>> We have a guide on applying here:
>> http://wiki.openchemistry.org/Applying_to_GSoC
>>
>> There are several excellent guides to molecular mechanics force fields
>> out on the web, but you might want to look here:
>>
>> http://vergil.chemistry.gatech.edu/courses/chem6485/pdf/molmech-lecture.pdf
>>
>> There are two approaches to consider for the project:
>> 1) Adapting an existing force field package (e.g., OpenMM) for other
>> molecular force fields - for example using Open Babel's current force field
>> implementation to export parameters and custom force types to OpenMM XML
>> format.
>>
>> 2) Replacing the current code in Open Babel with a new implementation
>> that is designed to be optimization-friendly, vectorized, and OpenMP-ready.
>> (i.e., it breaks the molecule into work-groups to run on OpenMP or OpenCL
>> threads).
>>
>> Hope that helps,
>> -Geoff
>
>
>
>
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