MDS 0.5.0 -> 0.6.1?

Oliver Beckstein

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Jul 26, 2016, 8:18:43 PM7/26/16

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Hi,

I have some sims from the MDS 0.5.0 days, which looks like the following (see below); the state files appear to be h5 and not jsonn. The 0.5.1 converter script appears to want json state files.

How can I upgrade to MDS 0.6.1?

Oliver

%ls /Users/oliver/Projects/Transporters/Mhp1/Simulations/Mhp1/*/*

/Users/oliver/Projects/Transporters/Mhp1/Simulations/Mhp1/GROMOS96/Group.cec321d5-0604-49c2-8c6a-2d04cad7a565.h5
/Users/oliver/Projects/Transporters/Mhp1/Simulations/Mhp1/OPLSAA/Group.6847a0ab-60f6-4bb5-a2ae-33973961d9c1.h5
/Users/oliver/Projects/Transporters/Mhp1/Simulations/Mhp1/all/Group.b1ccc68f-ebba-4e4e-8c98-18c3fc7ff076.h5

/Users/oliver/Projects/Transporters/Mhp1/Simulations/Mhp1/GROMOS96/Mhp1-WT-IF-NA-BNZ-MD_001:
Sim.9e219710-7637-4d54-9867-64b73c5abe58.h5

accessibility
/

edges
/

mean_radial_histogram
/

water_accessibility
/

/Users/oliver/Projects/Transporters/Mhp1/Simulations/Mhp1/GROMOS96/Mhp1-WT-IF-NA-BNZ-MD_002:
Sim.55a2c156-09a0-48bd-b4b8-b6132e7a53b1.h5

accessibility
/

edges
/

mean_radial_histogram
/

water_accessibility/

--
Oliver Beckstein * orbe...@gmx.net
skype: orbeckst * orbe...@gmail.com

Max Linke

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Jul 27, 2016, 10:05:13 AM7/27/16

to datreant

Did you try https://github.com/datreant/mds-0.5.0-to-0.6.0 ?

David Dotson

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Jul 28, 2016, 2:30:28 PM7/28/16

to datreant

There's also pytables-to-json, which is what you will need to create JSON state files from the old HDF5 ones. However, this script has not been updated to reflect changes in MDSynthesis from MDS 0.6.0, in particular single-universe treatment.

If this is still an issue for you, Oliver, I can fix up pytables-to-json.py to give state files that work with current MDSynthesis. It won't be hard, since most of what's changed is already reflected in mds-0.5.0-to-0.6.0.py

David

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