multi-ego - beta.5

meGO - Molten Globule

This is the first version of the new generation of multi-eGO that uses a more informative prior than the previous random-coil model This is to have a reference implementation before the next release that includes a full reparameterisation of the local interactions and new repulsions rules

What's Changed

• all-vs-all MG by @carlocamilloni in https://github.com/multi-ego/multi-eGO/pull/481
• fran changes + small fixes + working makemat by @brunostega in https://github.com/multi-ego/multi-eGO/pull/484
• added stuff for regtest, fixed topology reading and c6 c12 mapping by @brunostega in https://github.com/multi-ego/multi-eGO/pull/486
• fixes to mg prior and to account for neighbor excluded AA by @carlocamilloni in https://github.com/multi-ego/multi-eGO/pull/504
• regtest case with two prior folders by @carlocamilloni in https://github.com/multi-ego/multi-eGO/pull/505
• better IO sorting by @carlocamilloni in https://github.com/multi-ego/multi-eGO/pull/507
• Bkbn h by @brunostega in https://github.com/multi-ego/multi-eGO/pull/512
• added H to other amino acids, fixed c12 H and tuned ALA dihedrals by @brunostega in https://github.com/multi-ego/multi-eGO/pull/513
• corrected PRO, changed HN to H for ff consistensy, modified mdmat and cmdata by @brunostega in https://github.com/multi-ego/multi-eGO/pull/514
• Addition of masks and c6 c12 of H by @brunostega in https://github.com/multi-ego/multi-eGO/pull/515
• New sigma prior by @carlocamilloni in https://github.com/multi-ego/multi-eGO/pull/516
• updated c6/c12 oh by @carlocamilloni in https://github.com/multi-ego/multi-eGO/pull/517
• Corrected epsilon sigma reading in nonbonded parameters with parmed by @brunostega in https://github.com/multi-ego/multi-eGO/pull/520
• new input by @brunostega in https://github.com/multi-ego/multi-eGO/pull/522
• Code cleaning, better input reading and fixed intra-domain tool and flag handling. Tested on lysozyme 2 domain by @brunostega in https://github.com/multi-ego/multi-eGO/pull/523
• fixed --zero flag by @brunostega in https://github.com/multi-ego/multi-eGO/pull/536
• make_mat.py with h5 input by @carlocamilloni in https://github.com/multi-ego/multi-eGO/pull/537
• hdf5 and more by @carlocamilloni in https://github.com/multi-ego/multi-eGO/pull/545
• New epsilon by @carlocamilloni in https://github.com/multi-ego/multi-eGO/pull/546
• New epsilon by @carlocamilloni in https://github.com/multi-ego/multi-eGO/pull/547
• regtests by @carlocamilloni in https://github.com/multi-ego/multi-eGO/pull/548
• New epsilon by @carlocamilloni in https://github.com/multi-ego/multi-eGO/pull/549
• fixes about ptolearn and eps_min by @carlocamilloni in https://github.com/multi-ego/multi-eGO/pull/551
• more control over sigma ranges in both attractive and repulsive interactions by @carlocamilloni in https://github.com/multi-ego/multi-eGO/pull/552
• improve intra/inter symmetrization by @carlocamilloni in https://github.com/multi-ego/multi-eGO/pull/553
• new set of Dihedrals with c12 rep in ensemble and make mat by @brunostega in https://github.com/multi-ego/multi-eGO/pull/554

Full Changelog: https://github.com/multi-ego/multi-eGO/compare/prior_rc...beta5

- Python
Published by carlocamilloni about 1 year ago

multi-ego - prior_rc

multi-eGO prior_rc version

this release is associated with the latest version of the first generation of multi-eGO the second generation of the model is based on the new molten-globule prior and may become not compatible with this first generation

What's Changed

• new io format by @frantropy in https://github.com/multi-ego/multi-eGO/pull/461
• new d aminoacids by @frantropy in https://github.com/multi-ego/multi-eGO/pull/468
• Code refactoring and optimisation by @carlocamilloni in https://github.com/multi-ego/multi-eGO/pull/469
• fix to general repulsion rule and updated regtest by @carlocamilloni in https://github.com/multi-ego/multi-eGO/pull/482
• added resdata and CM pbc warning by @brunostega in https://github.com/multi-ego/multi-eGO/pull/483
• make_mat modification for cmdata compatibility by @brunostega in https://github.com/multi-ego/multi-eGO/pull/495
• fix for cross interaction by @carlocamilloni

Full Changelog: https://github.com/multi-ego/multi-eGO/compare/beta4...prior_rc

- Python
Published by carlocamilloni over 1 year ago

multi-ego - beta.4

This is the fourth beta release of the multi-eGO toolkit and parameters

The changes are mostly fixes and enhancement related to systems made by multiple molecules from multiple specie

What's Changed

• updated rules for cross learning intra/intermolecular interactions by @carlocamilloni in https://github.com/multi-ego/multi-eGO/pull/426
• Fixed user pair bug in make mat for more than one other molecule type by @gaiaperaja in https://github.com/multi-ego/multi-eGO/pull/437
• Fixed indexing error which broke residue indexing when more than one … by @gaiaperaja in https://github.com/multi-ego/multi-eGO/pull/438
• cmdata fixes for pbc and cross by @gaiaperaja in https://github.com/multi-ego/multi-eGO/pull/441
• multi-epsilon merge from main by @carlocamilloni in https://github.com/multi-ego/multi-eGO/pull/442
• Right nomenclature dppc, chol new dihedrals, chol itp by @gaiaperaja in https://github.com/multi-ego/multi-eGO/pull/447
• added cholesterol to lipids.rtp by @gaiaperaja in https://github.com/multi-ego/multi-eGO/pull/448
• Fix three systems cmdata by @frantropy in https://github.com/multi-ego/multi-eGO/pull/449
• Feature/residue make mat by @frantropy in https://github.com/multi-ego/multi-eGO/pull/460
• more get_box options by @carlocamilloni in https://github.com/multi-ego/multi-eGO/pull/462

Full Changelog: https://github.com/multi-ego/multi-eGO/compare/beta3...beta4

- Python
Published by carlocamilloni over 1 year ago

multi-ego - beta.3

This is the third beta release of the multi-eGO toolkit and parameters

The main changes are the following:

• New distance estimate when training/reference data have poor statistics
• Improved merging rules for repulsive interactions
• intra and inter domain contacts now are fully decoupled (i.e. separated mdthreshold/rcthreshold)
• added calcium parameters and matrix compatibility check by @brunostega in https://github.com/multi-ego/multi-eGO/pull/433
• Multi epsilon input files by @brunostega in https://github.com/multi-ego/multi-eGO/pull/439

Full Changelog: https://github.com/multi-ego/multi-eGO/compare/beta2...beta3

- Python
Published by carlocamilloni about 2 years ago

multi-ego - beta.2

This is the second beta release of the multi-eGO toolkit and parameters

The main changes are the following:

• Fix for the mass of aromatic rings plus some code cleaning by @carlocamilloni in https://github.com/multi-ego/multi-eGO/pull/274
• Moved from epsilon fraction to epsilon_min by @carlocamilloni in https://github.com/multi-ego/multi-eGO/pull/276
• Added different domain epsilon by @frantropy in https://github.com/multi-ego/multi-eGO/pull/280
• Simplified input flags by @carlocamilloni in https://github.com/multi-ego/multi-eGO/pull/298
• Fix for N-terminus proline by @carlocamilloni in https://github.com/multi-ego/multi-eGO/pull/330
• Simplified handling of disulphide bridges by @carlocamilloni in https://github.com/multi-ego/multi-eGO/pull/333
• Feature/compression io by @frantropy in https://github.com/multi-ego/multi-eGO/pull/334
• New CMDATA implementation @frantropy
• New way to handle equivalent atoms @carlocamilloni
• Improved the merging of multiple training data @carlocamilloni
• Better handling of cross interactions (molecules of different species) @brunostega
• Fixed issue with single atom topologies @brunostega

New Contributors

• @gaiaperaja made their first contribution in https://github.com/multi-ego/multi-eGO/pull/304

Full Changelog: https://github.com/multi-ego/multi-eGO/compare/beta1...beta2

- Python
Published by carlocamilloni about 2 years ago

multi-ego - beta.1

This is the first beta release of the multi-eGO toolkit and parameters and is associated with the preprint version of "Multi-eGO: model improvements towards the study of complex self-assembly processes", https://doi.org/10.26434/chemrxiv-2023-67255

- Python
Published by carlocamilloni over 2 years ago