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CHARMM parsers #9

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dotsdl opened this issue Feb 6, 2017 · 6 comments
Open

CHARMM parsers #9

dotsdl opened this issue Feb 6, 2017 · 6 comments

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@dotsdl
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dotsdl commented Feb 6, 2017

In line with the overall API proposal, we want to have parsers for each of the major MD engines, and eventually have coverage for all of those in use. Since there are essentially two types of estimators (TI and FEP), each packages needs a parser for:

  1. Extracting reduced potentials u_nk from output files (for FEP).
  2. Extracting derivatives DHdl from output files (for TI).

This issue is the nexus for discussion for such parsers for the CHARMM package. If you have existing parsing code for this package, comment below and we can begin adapting it into the parsers outlined above in a PR.

@davidlmobley
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@donghyuksuh - is there someone on the CHARMM side you would recommend who might be interested in contributing code towards a CHARMM parser as part of a python library for general analysis of alchemical free energy calculations? I'm thinking there may be someone in the Roux group, perhaps you?

@donghyuksuh
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donghyuksuh commented Feb 9, 2017 via email

@davidlmobley
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@donghyuksuh - none of us are CHARMM users, as far as I am aware, nor do we have energy gradient files, so if you could provide some sample files and, perhaps, your modified parser, that would be very helpful.

@donghyuksuh
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donghyuksuh commented Feb 9, 2017 via email

@dotsdl
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dotsdl commented Feb 9, 2017

Are there any standard-ish ways that outputs for alchemical free energy runs are done in CHARMM, or is this something that is done ad hoc each time depending on the script used? If it's the latter, then we can still build parsers, and in the docs for the CHARMM parser we can include instructions for how one should output data so the parsers can easily ingest it.

@dotsdl dotsdl mentioned this issue Feb 9, 2017
@donghyuksuh
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donghyuksuh commented Feb 9, 2017 via email

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