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

Full Changelog: prior_rc...beta5

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 #461
• new d aminoacids by @frantropy in #468
• Code refactoring and optimisation by @carlocamilloni in #469
• fix to general repulsion rule and updated regtest by @carlocamilloni in #482
• added resdata and CM pbc warning by @brunostega in #483
• make_mat modification for cmdata compatibility by @brunostega in #495
• fix for cross interaction by @carlocamilloni

Full Changelog: beta4...prior_rc

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

Full Changelog: beta3...beta4

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 md_threshold/rc_threshold)
• added calcium parameters and matrix compatibility check by @brunostega in #433
• Multi epsilon input files by @brunostega in #439

Full Changelog: beta2...beta3

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 #274
• Moved from epsilon fraction to epsilon_min by @carlocamilloni in #276
• Added different domain epsilon by @frantropy in #280
• Simplified input flags by @carlocamilloni in #298
• Fix for N-terminus proline by @carlocamilloni in #330
• Simplified handling of disulphide bridges by @carlocamilloni in #333
• Feature/compression io by @frantropy in #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 #304

Full Changelog: beta1...beta2

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