Print dipol vectors

Saurabh Belsare · Post by **Saurabh Belsare** » Wed Dec 09, 2015 5:45 pm

Hi Peter,

I've found the function which returns the induced dipoles, and was able to use it. I was also wondering about the permanent dipoles in order to get the total dipole for each atom in the system. Lee-Ping mentioned in his last post on this thread that it would have to be implemented, and outlined the procedure. If it hasn't been implemented, I'll see if I can put it in following his steps, and based on the OpenMMDeveloperGuide.

Thanks.
Saurabh

Peter Eastman · Post by **Peter Eastman** » Wed Dec 09, 2015 7:40 pm

That would be great! If you have questions about the code, feel free to ask. The AMOEBA code is not a model of clarity, unfortunately!

Peter

Saurabh Belsare · Post by **Saurabh Belsare** » Mon Dec 14, 2015 1:38 pm

Hi Peter,

I've forked and cloned the git repo, and am working on implementing the function. However, I was wondering how I should compile the code to test whatever I am coding up. The installation instructions in the user guide only outline the installations for the binaries, and I can't find any obvious makefiles in the source repo I've cloned to make the code.

Thanks.
Saurabh

Peter Eastman · Post by **Peter Eastman** » Mon Dec 14, 2015 2:11 pm

The user guide has a whole chapter on compiling from source. See http://docs.openmm.org/6.3.0/userguide/ ... ource-code.

Peter

Saurabh Belsare · Post by **Saurabh Belsare** » Tue Feb 02, 2016 1:55 am

Hi Peter,

I've implemented the function to get permanent dipoles in the lab frame on both, the reference and CUDA platforms. I've checked the results manually against TINKER for a pure water box, and they match. Should I submit a pull request?

Thanks.
Saurabh

Saurabh Belsare · Post by **Saurabh Belsare** » Thu Jun 30, 2016 1:56 pm

Hi Dr. Eastman,

I've implemented my own functions to get both, the permanent and total dipoles in a source version I had forked from the github repo when it was OpenMM 6.3. I am now using OpenMM 7 (from conda, not from source) and want to use these functions in that version as well.

I've checked the results manually against TINKER for a pure water box, and they match. Could I submit a pull request for my code, and you could merge those functions into the current version of OpenMM? Or is there some other way you would suggest that I go about it? Because otherwise I would have to rewrite those functions each time I upgrade my version of OpenMM.

Thank you.

Saurabh

Peter Eastman · Post by **Peter Eastman** » Thu Jun 30, 2016 3:01 pm

A pull request will be great. Thanks!

Peter

Saurabh Belsare · Post by **Saurabh Belsare** » Thu Jun 30, 2016 3:20 pm

Hi Dr. Eastman,

I've created a pull request.

Thanks.

Saurabh

Print dipol vectors

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