- 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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- May 20, 2021
- Mar 05, 2021
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cmaffeo2 authored
Connections between ssDNA and dsDNA should now always be of the type 'sscrossover', never 'intrahelical' The latter could result in bonds between the end of dsDNA and ssDNA from forming if the dsDNA end was also bound to another helix, but this may remain an issue for three-way dsDNA junctions.
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cmaffeo2 authored
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- Mar 02, 2021
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cmaffeo2 authored
Added box_type=orthogonal and CUDA_DEVICE={gpu} to oxDNA input file; thanks to Elija Feigl for bringing the issue to our attention
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cmaffeo2 authored
Ensure no duplicate bonds in ENM, logging violations; thanks to Elija Feigl for bringing duplicate bonds to our attention
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cmaffeo2 authored
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cmaffeo2 authored
Updated ENM to avoid situation where network is applied to single-stranded DNA at end of double-stranded helix
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cmaffeo2 authored
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cmaffeo2 authored
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- Feb 10, 2021
- Dec 07, 2020
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cmaffeo2 authored
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- Dec 03, 2020