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Created with Raphaël 2.2.027Oct252128Sep13Jul20May5Mar210Feb7Dec320Aug28Jul10Jun522Apr18Mar95328Feb2524211918128724Jan227212Dec618Nov31Oct927Sep26255427Aug201310Jul10May30Apr8525Mar21158Feb129Jan19321Dec189215Nov417Oct129Sep282725232221201918171514131110765429Aug2824212017131023Jul2018171613106328Jun1514139Apr754130Mar27232221202128Feb2621Dec2017Oct18Sep31Aug30112124Jul2018131211107629Jun2827261514138131May2910Apr754329Mar2726128Feb262423222120191716153Escape '%' sign in mrdna script help statements; thanks to Elija Feigl for the catchRevert "Add mrdna.simulate.multiresolution_simulation(...,center_object = True,...) to center objects at each step during multiresolution simulations, avoiding drift to locations where PDB format cannot be used"Add mrdna.simulate.multiresolution_simulation(...,center_object = True,...) to center objects at each step during multiresolution simulations, avoiding drift to locations where PDB format cannot be usedAdded option to specify custom persistence length to mrdna script for first 25% of coarse simulationOptionally write PQR filesExpose enrg_md_steps option in mrdna and enrgmd scripts and in mrdna.simulate.multiresolution_simulation(); thanks to Elija Feigl for the suggestionMake correct use of "gpu" option in SegmentModel.simulate_oxdna(); thanks to Elija Feigl catching the issueAdd 'arbd' argument to model.simulate()Enable group site restraintsMove charmm files to arbdmodel. Wrap write_release_version() in try/exceptFix multiple issues related to strand generation, also reduce timestep to 100fs if coarse_local_twist==TrueVarious changes to segmentmodel, mostly involving deletion of DNAExposed fill_sequence in read_cadnanoCheck for '?' in Strand.set_sequence()Added fill_sequence parameter to SegmentModel.set_sequence and to the mrdna and enrgmd scripts, with default value 'T', since that is most common for origami. Thanks to Elija Feigl for recommending the change.Connections between ssDNA and dsDNA should now always be of the type 'sscrossover', never 'intrahelical'Write out ENM bonds in blocks according to residue pair type such as stack, (base)pair, etcAdded box_type=orthogonal and CUDA_DEVICE={gpu} to oxDNA input file; thanks to Elija Feigl for bringing the issue to our attentionEnsure no duplicate bonds in ENM, logging violations; thanks to Elija Feigl for bringing duplicate bonds to our attentionAdded basic configuration for loggingUpdated ENM to avoid situation where network is applied to single-stranded DNA at end of double-stranded helixDecreased length of T-junction bond from crossover distance of 18.5 to more reasonable 12.5Fixed arguments in _rescale_splines callAdded logic to skip ssDNA in _get_intrahelical_neighbor, fixing ENMAdded support for ARBD group sitesFixed two small bugs, one involving use of is for string comparison, the other involving an incorrect function call when a restraint is added to the system with only one argumentFixed small bug introduced in 6446299Fix to productpotentialExposed seq_dep_file option for oxDNAAdded external_forces_file option to simulate_oxdnaAdded option to exclude interhelical bonds from atomic ENMAdded convenience function to Segments and SegmentModel to select blunt DNA endsFixed ENM so it produces bonds across intrahelical connectionsAdded one_bea_per_monomer option to generate_bead_modelAdded some convenience routines for pulling infomration from strandsAdded support to arbdmodel for product potentialsUpdated bondAngle to be two angles, one bondInitial commit of bondAngle (one angle, two bonds)Fixed model_from_lists for 3'-to-5' structures; fixed issue with single-nucleotide 'crossovers'; added debug flag for tracing strandsFixed oxDNA topology for circular strands; increased default max_backbone_force