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rmcgibbo / openmm-cmd

OpenMM Command Line Application
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We should be ready for a beta test. #7

Closed leeping closed 11 years ago

leeping commented 11 years ago

Hi Robert,

I added nine example calculations along with instructions on how to run them. I think the script should be ready for a public beta test now, but testers need to have the most recent development build of OpenMM.

Thanks,

rmcgibbo commented 11 years ago

This is awesome. All the amoeba and xml options look great.

rmcgibbo commented 11 years ago

Do you know off the top of your head what the features are that require the dev. build? One of them is obviously the pickle restart reporter, but if we switch to JSON that will be solved.

leeping commented 11 years ago

The anisotropic barostat is another one.

On Aug 11, 2013, at 1:19 PM, Robert McGibbon notifications@github.com wrote:

Do you know off the top of your head what the features are that require the dev. build? One of them is obviously the pickle restart reporter, but if we switch to JSON that will be solved.

— Reply to this email directly or view it on GitHub.

rmcgibbo commented 11 years ago

Okay. I'll tag a release and write up something that can be sent out on email/forums. 

-Robert Sent from my iPhone.

On Sun, Aug 11, 2013 at 2:43 PM, Lee-Ping notifications@github.com wrote:

The anisotropic barostat is another one.

  • Lee-Ping On Aug 11, 2013, at 1:19 PM, Robert McGibbon notifications@github.com wrote:

    Do you know off the top of your head what the features are that require the dev. build? One of them is obviously the pickle restart reporter, but if we switch to JSON that will be solved.

    — Reply to this email directly or view it on GitHub.

    Reply to this email directly or view it on GitHub: https://github.com/rmcgibbo/openmm-cmd/issues/7#issuecomment-22466018

leeping commented 11 years ago

Hi Robert,

You can remove the anisotropic barostat from the examples if you want (or add a note in About.txt). I imagine all the other examples should work with OpenMM 5.1 .

Thanks,

On Aug 11, 2013, at 2:47 PM, Robert McGibbon wrote:

Okay. I'll tag a release and write up something that can be sent out on email/forums.

-Robert Sent from my iPhone.

On Sun, Aug 11, 2013 at 2:43 PM, Lee-Ping notifications@github.com wrote:

The anisotropic barostat is another one.

  • Lee-Ping On Aug 11, 2013, at 1:19 PM, Robert McGibbon notifications@github.com wrote:

    Do you know off the top of your head what the features are that require the dev. build? One of them is obviously the pickle restart reporter, but if we switch to JSON that will be solved.

    — Reply to this email directly or view it on GitHub.

    Reply to this email directly or view it on GitHub: https://github.com/rmcgibbo/openmm-cmd/issues/7#issuecomment-22466018 — Reply to this email directly or view it on GitHub.

rmcgibbo commented 11 years ago

Maybe we can do a version check inside the script? I'll install the 5.1 release version and make sure all the examples run with it or give an informative error saying why they don't run.

Sent from my iPhone

On Aug 11, 2013, at 3:05 PM, Lee-Ping notifications@github.com wrote:

Hi Robert,

You can remove the anisotropic barostat from the examples if you want (or add a note in About.txt). I imagine all the other examples should work with OpenMM 5.1 .

Thanks,

  • Lee-Ping

On Aug 11, 2013, at 2:47 PM, Robert McGibbon wrote:

Okay. I'll tag a release and write up something that can be sent out on email/forums.

-Robert Sent from my iPhone.

On Sun, Aug 11, 2013 at 2:43 PM, Lee-Ping notifications@github.com
wrote:

The anisotropic barostat is another one.

  • Lee-Ping On Aug 11, 2013, at 1:19 PM, Robert McGibbon notifications@github.com wrote:

    Do you know off the top of your head what the features are that require the dev. build? One of them is obviously the pickle restart reporter, but if we switch to JSON that will be solved.

    — Reply to this email directly or view it on GitHub.

    Reply to this email directly or view it on GitHub: https://github.com/rmcgibbo/openmm-cmd/issues/7#issuecomment-22466018 — Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHub.

leeping commented 11 years ago

Sure, I think that's a good way to go. :)

On Aug 11, 2013, at 3:14 PM, Robert McGibbon wrote:

Maybe we can do a version check inside the script? I'll install the 5.1 release version and make sure all the examples run with it or give an informative error saying why they don't run.

Sent from my iPhone

On Aug 11, 2013, at 3:05 PM, Lee-Ping notifications@github.com wrote:

Hi Robert,

You can remove the anisotropic barostat from the examples if you want (or add a note in About.txt). I imagine all the other examples should work with OpenMM 5.1 .

Thanks,

  • Lee-Ping

On Aug 11, 2013, at 2:47 PM, Robert McGibbon wrote:

Okay. I'll tag a release and write up something that can be sent out on email/forums.

-Robert Sent from my iPhone.

On Sun, Aug 11, 2013 at 2:43 PM, Lee-Ping notifications@github.com wrote:

The anisotropic barostat is another one.

  • Lee-Ping On Aug 11, 2013, at 1:19 PM, Robert McGibbon notifications@github.com wrote:

    Do you know off the top of your head what the features are that require the dev. build? One of them is obviously the pickle restart reporter, but if we switch to JSON that will be solved.

    — Reply to this email directly or view it on GitHub.

    Reply to this email directly or view it on GitHub: https://github.com/rmcgibbo/openmm-cmd/issues/7#issuecomment-22466018 — Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHub. — Reply to this email directly or view it on GitHub.

leeping commented 11 years ago

Also, feel free to switch to json if you want, which should enable the "restart" example for 5.1 users. It should be as simple as "import json as pickle", although that might be misleading for readers of the code. :)

On Aug 11, 2013, at 3:14 PM, Robert McGibbon wrote:

Maybe we can do a version check inside the script? I'll install the 5.1 release version and make sure all the examples run with it or give an informative error saying why they don't run.

Sent from my iPhone

On Aug 11, 2013, at 3:05 PM, Lee-Ping notifications@github.com wrote:

Hi Robert,

You can remove the anisotropic barostat from the examples if you want (or add a note in About.txt). I imagine all the other examples should work with OpenMM 5.1 .

Thanks,

  • Lee-Ping

On Aug 11, 2013, at 2:47 PM, Robert McGibbon wrote:

Okay. I'll tag a release and write up something that can be sent out on email/forums.

-Robert Sent from my iPhone.

On Sun, Aug 11, 2013 at 2:43 PM, Lee-Ping notifications@github.com wrote:

The anisotropic barostat is another one.

  • Lee-Ping On Aug 11, 2013, at 1:19 PM, Robert McGibbon notifications@github.com wrote:

    Do you know off the top of your head what the features are that require the dev. build? One of them is obviously the pickle restart reporter, but if we switch to JSON that will be solved.

    — Reply to this email directly or view it on GitHub.

    Reply to this email directly or view it on GitHub: https://github.com/rmcgibbo/openmm-cmd/issues/7#issuecomment-22466018 — Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHub. — Reply to this email directly or view it on GitHub.

rmcgibbo commented 11 years ago

Yeah, I think switching to json is probably a good move for robustness and cross platform type stuff. But -1 on import json as pickle :)

-Robert Sent from my iPhone.

On Sun, Aug 11, 2013 at 3:16 PM, Lee-Ping notifications@github.com wrote:

Also, feel free to switch to json if you want, which should enable the "restart" example for 5.1 users. It should be as simple as "import json as pickle", although that might be misleading for readers of the code. :) On Aug 11, 2013, at 3:14 PM, Robert McGibbon wrote:

Maybe we can do a version check inside the script? I'll install the 5.1 release version and make sure all the examples run with it or give an informative error saying why they don't run.

Sent from my iPhone

On Aug 11, 2013, at 3:05 PM, Lee-Ping notifications@github.com wrote:

Hi Robert,

You can remove the anisotropic barostat from the examples if you want (or add a note in About.txt). I imagine all the other examples should work with OpenMM 5.1 .

Thanks,

  • Lee-Ping

On Aug 11, 2013, at 2:47 PM, Robert McGibbon wrote:

Okay. I'll tag a release and write up something that can be sent out on email/forums.

-Robert Sent from my iPhone.

On Sun, Aug 11, 2013 at 2:43 PM, Lee-Ping notifications@github.com wrote:

The anisotropic barostat is another one.

  • Lee-Ping On Aug 11, 2013, at 1:19 PM, Robert McGibbon notifications@github.com wrote:

    Do you know off the top of your head what the features are that require the dev. build? One of them is obviously the pickle restart reporter, but if we switch to JSON that will be solved.

    — Reply to this email directly or view it on GitHub.

    Reply to this email directly or view it on GitHub: https://github.com/rmcgibbo/openmm-cmd/issues/7#issuecomment-22466018 — Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHub. — Reply to this email directly or view it on GitHub.

Reply to this email directly or view it on GitHub: https://github.com/rmcgibbo/openmm-cmd/issues/7#issuecomment-22466589