- 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
- Aug 20, 2020
- Jul 28, 2020
- Jun 10, 2020
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cmaffeo2 authored
Made cadnano reader set azimuthal angle more accurately; some problems could arise with cadnano2 files that are saved in cadnano2.5 due to incorrect assignment of eulerZ in cadnano2.5
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cmaffeo2 authored
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cmaffeo2 authored
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cmaffeo2 authored
Removed os.sync() lines prior to running arbd/oxDNA simulations because they can hang indefinitely; needs testing
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cmaffeo2 authored
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- Jun 05, 2020
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cmaffeo2 authored
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- Apr 22, 2020
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cmaffeo2 authored
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- Mar 18, 2020
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cmaffeo2 authored
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- Mar 09, 2020
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cmaffeo2 authored
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- Mar 05, 2020
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cmaffeo2 authored
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