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
Print dipol vectors
- Peter Eastman
- Posts: 2577
- Joined: Thu Aug 09, 2007 1:25 pm
Re: Print dipol vectors
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
Peter
- Saurabh Belsare
- Posts: 32
- Joined: Sat Aug 14, 2010 8:43 am
Re: Print dipol vectors
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
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
- Posts: 2577
- Joined: Thu Aug 09, 2007 1:25 pm
Re: Print dipol vectors
The user guide has a whole chapter on compiling from source. See http://docs.openmm.org/6.3.0/userguide/ ... ource-code.
Peter
Peter
- Saurabh Belsare
- Posts: 32
- Joined: Sat Aug 14, 2010 8:43 am
Re: Print dipol vectors
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
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
- Posts: 32
- Joined: Sat Aug 14, 2010 8:43 am
Re: Print dipol vectors
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
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
- Posts: 2577
- Joined: Thu Aug 09, 2007 1:25 pm
Re: Print dipol vectors
A pull request will be great. Thanks!
Peter
Peter
- Saurabh Belsare
- Posts: 32
- Joined: Sat Aug 14, 2010 8:43 am
Re: Print dipol vectors
Hi Dr. Eastman,
I've created a pull request.
Thanks.
Saurabh
I've created a pull request.
Thanks.
Saurabh