lorenzo-rovigatti oxDNA issues

lorenzo-rovigatti / oxDNA

A new version of the code to simulate the oxDNA/oxRNA models, now equipped with Python bindings

https://dna.physics.ox.ac.uk/

GNU General Public License v3.0

38 stars 26 forks source link

issues

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[DOCUMENTATION] Sequence Dependence of Cross-Stacking

#108 alec-cook opened 5 days ago
1
Compute energy without running the simulation

#107 swapnilbaral-git opened 3 weeks ago
1
Pull

#106 Subhajit-Roy-Partho closed 4 weeks ago
1
[BUG] Build failure with cuda 12.5.0

#105 micwoj92 opened 1 month ago
1
oxDNA analysis tool: duplex angle plotter

#104 AdaABen opened 1 month ago
2
Bump jinja2 from 3.0.3 to 3.1.4 in /docs

#103 dependabot[bot] closed 1 month ago
0
"Segmentation fault" when running oxDNA with an external force file on MPI.

#102 FujiwaraRobert opened 2 months ago
6
Can't read configuration file from the examples [v3.6.1]

#101 A-VER closed 2 months ago
2
Add 'precision' non-mandatory option for ForceEnergy and PotentialEnergy observables

#100 mlsample closed 1 month ago
9
Added non-mandatory option 'precision' to the ForceEnergy and PotentalEnergy observables

#99 mlsample closed 2 months ago
1
[BUG] Rye Reader method `inbox` does not move all points inside the box

#98 JeDeveloper closed 2 months ago
1
[BUG] oxpy - FFS Simulation Type Fails to Log Correctly When Running Consecutive Processes

#97 JeDeveloper closed 3 months ago
1
observable structure factor not found

#96 AdaABen closed 3 months ago
1
oxDNA observable: radial distribution function

#95 AdaABen closed 2 months ago
2
[BUG] Insufficient Oxpy Cmake Error Message

#94 JeDeveloper opened 3 months ago
1
fixed rcut for unbonded pair

#93 tgfrancesco closed 3 months ago
0
> Thanks for the report! That’s a bug on my part but I won’t have a computer for the next few weeks. You can get around it by adding the line `use_average_seq = 1` to your input file.

#92 Azzzzzz11 closed 3 months ago
11
[BUG???] get_vectors_from_quat() different than ouldridge(2011, p.152) phd thesis and rapaport (1985)

#91 alphataubio closed 4 months ago
1
How to devide the HB ENERGY into each DNA molecules

#90 masakikato001 closed 5 months ago
2
[BUG] analysis/tests/test.sh missing files

#89 siegmundbio closed 5 months ago
7
Merge back some small changes

#88 lorenzo-rovigatti closed 5 months ago
0
Can a backbone connection be approximated with mutual harmonic traps?

#87 alec-cook closed 5 months ago
7
[BUG] oxDNA can not run on GPU

#86 TruongChien closed 6 months ago
2
[BUG] Parallel Tempering_MPI example results (energy, trajectory ..) are not evolving

#85 hub-Veronika closed 3 months ago
7
[BUG] Installation, unable to build with make command

#84 sheneric88 closed 6 months ago
4
[FEATURE REQUEST] Can we adjust the range of Debye cutoff?

#83 churchyuan closed 6 months ago
6
[BUG] Trouble installing oxDNA

#82 mrland99 closed 6 months ago
4
DRH -> NA change in DRHInteraction_relax

#81 eryykr closed 7 months ago
0
Import oxDNA to Blender using Molecular Nodes

#80 BradyAJohnston closed 7 months ago
12
Changing name of interaction_type for hybrids

#79 eryykr closed 7 months ago
1
Error handling for truncated configurations in oat's trajectory parser

#78 ErikPoppleton closed 8 months ago
0
Solves variadic error caused by clang compilers.

#77 Subhajit-Roy-Partho closed 8 months ago
2
[BUG] stuck during doing confGenerator with .top file that contains circular DNA

#76 Dot233 closed 8 months ago
3
Selectively disabling steric interactions

#75 Alec-physics closed 8 months ago
4
Benchmarking performance: hilbert sorting, lists, force, thermostat etc

#74 swapnilbaral-git closed 8 months ago
5
Shift harmonic force pos the same way as NT pos

#73 RodenLuo closed 5 months ago
1
DNA-RNA hybrids

#72 lorenzo-rovigatti closed 8 months ago
1
[Bug] How to set `pos0` for a harmonic trap?

#71 RodenLuo closed 5 months ago
17
Subhajit roy partho patch 1

#70 Subhajit-Roy-Partho closed 9 months ago
0
New Topology Format

#69 ErikPoppleton closed 9 months ago
3
DNA-RNA hybrid model

#68 eryykr closed 9 months ago
9
[BUG] Truncated trajectory

#67 Boyu-Liu03 closed 9 months ago
4
Update pybind

#66 ErikPoppleton closed 9 months ago
0
[BUG] oxpy `file_info` segfaults when presented with a malformed trajectory file

#65 JeDeveloper closed 8 months ago
2
Modifying existing external force definition

#64 TheAutoMan1ac closed 10 months ago
4
[BUG] Relaxation of DNA structures behaves differently between recent oxDNA versions and the old one on oxServe

#63 ErikPoppleton opened 10 months ago
2
make: *** No rule to make target install. Stop.

#62 jmarlhens closed 1 year ago
2
Oat dev

#61 ErikPoppleton closed 1 year ago
0
UnicodeDecodeError when running FFS

#60 naliio closed 1 year ago
6
Getting error when installing

#59 naliio closed 1 year ago
7