- Aug 27, 2024
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cmaffeo2 authored
Make generate_bead_model use one_bead_per_monomer=True by default with max 1 bead per nt and bp, otherwise False
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- Aug 24, 2024
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cmaffeo2 authored
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- Jul 25, 2024
- Mar 26, 2024
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cmaffeo2 authored
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- Dec 01, 2023
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cmaffeo2 authored
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- Nov 22, 2023
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cmaffeo2 authored
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- Nov 16, 2023
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cmaffeo2 authored
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- Nov 14, 2023
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cmaffeo2 authored
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- Oct 29, 2023
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cmaffeo2 authored
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- Oct 26, 2023
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- Jul 27, 2023
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cmaffeo2 authored
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- Jul 20, 2023
- Jul 19, 2023
- Jul 10, 2023
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cmaffeo2 authored
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- May 11, 2023
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cmaffeo2 authored
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- Feb 13, 2023
- Nov 01, 2022
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cmaffeo2 authored
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- Oct 31, 2022
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cmaffeo2 authored
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- Feb 18, 2022
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Switch to static package build: replace setup.py with setup.cfg and pyproject.toml; update MANIFEST.in; remove mrdna/RELEASE-VERSION from .gitignore
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- Feb 07, 2022
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cmaffeo2 authored
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- Nov 29, 2021
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cmaffeo2 authored
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- Oct 29, 2021
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- Oct 28, 2021
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cmaffeo2 authored
Use average persistence length of parent segments in model.simulate(), rather than object returned _get_parent(), which can be 'model'; thanks to Elija Feigl
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- Oct 27, 2021
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cmaffeo2 authored
- Oct 25, 2021
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cmaffeo2 authored
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
- Oct 21, 2021
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cmaffeo2 authored
Added option to specify custom persistence length to mrdna script for first 25% of coarse simulation
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cmaffeo2 authored
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cmaffeo2 authored
Expose enrg_md_steps option in mrdna and enrgmd scripts and in mrdna.simulate.multiresolution_simulation(); thanks to Elija Feigl for the suggestion
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cmaffeo2 authored
Make correct use of "gpu" option in SegmentModel.simulate_oxdna(); thanks to Elija Feigl catching the issue
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cmaffeo2 authored
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cmaffeo2 authored
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cmaffeo2 authored
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- Sep 28, 2021
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cmaffeo2 authored
Fix multiple issues related to strand generation, also reduce timestep to 100fs if coarse_local_twist==True
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- Jul 13, 2021
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cmaffeo2 authored
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