Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / maccallumlab/meld issues and pull requests

#151 - Installation of MELD on ubuntu 22.04 (Cuda 12.0)

Issue - State: open - Opened by damax34 over 1 year ago

#150 - Select model feature in process_density_map script

Pull Request - State: open - Opened by kvr2007 over 1 year ago - 8 comments

#149 - error while running launch_remd

Issue - State: open - Opened by yoavatsmonraz over 1 year ago - 5 comments

#146 - Add tutorial to run simulation with cryo-EM data

Pull Request - State: closed - Opened by ccccclw over 1 year ago

#145 - building system from amber files

Issue - State: open - Opened by doesm over 1 year ago - 3 comments

#144 - Merge density map restraints feature

Pull Request - State: closed - Opened by ccccclw over 1 year ago - 6 comments

#143 - update with master

Pull Request - State: closed - Opened by jlmaccal over 1 year ago

#142 - Fix missing MAXFLOAT --> FLT_MAX

Pull Request - State: closed - Opened by meyersbs over 1 year ago

#139 - Add density map restraints support

Pull Request - State: closed - Opened by ccccclw almost 2 years ago - 2 comments

#137 - Implemented RDCs on CUDA and improved parameter sampling

Pull Request - State: closed - Opened by jlmaccal about 2 years ago

#136 - Improve mapper sampling

Pull Request - State: closed - Opened by jlmaccal about 2 years ago

#135 - Improve peak map sampling

Pull Request - State: closed - Opened by jlmaccal about 2 years ago

#134 - Implement Martini builder

Pull Request - State: closed - Opened by jlmaccal about 2 years ago

#133 - Issue Running MELD

Issue - State: open - Opened by nd346 about 2 years ago - 49 comments

#132 - Add support to generate velocities

Issue - State: open - Opened by splenz over 2 years ago
Labels: enhancement

#131 - Compile issues, on all OSs.

Issue - State: closed - Opened by colles2 over 2 years ago - 9 comments

#130 - Make rdcs work (slowly) with peak mapping

Pull Request - State: closed - Opened by jlmaccal over 2 years ago

#128 - Added convenience functions to add elastic network restraints by chain

Pull Request - State: closed - Opened by splenz over 2 years ago

#127 - Changed creation of virtual spin labels

Pull Request - State: closed - Opened by jlmaccal over 2 years ago

#126 - Added freeze_atoms and remove_potential

Pull Request - State: closed - Opened by jlmaccal over 2 years ago

#125 - Decoupled number of replicas from number of processes

Pull Request - State: closed - Opened by jlmaccal over 2 years ago

#124 - Implemented peak mapping handling into RDC restraint/transformer

Pull Request - State: closed - Opened by splenz over 2 years ago - 3 comments

#122 - Updated functions to include group_energy paramter when creating SystemStates

Pull Request - State: closed - Opened by splenz over 2 years ago - 1 comment

#121 - Global_rdc

Pull Request - State: closed - Opened by jlmaccal over 2 years ago

#120 - Update tutorials

Issue - State: open - Opened by jlmaccal over 2 years ago

#119 - De parmed ify

Pull Request - State: closed - Opened by jlmaccal over 2 years ago

#118 - Change patchers

Issue - State: closed - Opened by jlmaccal over 2 years ago
Labels: enhancement

#117 - Revise indexing

Issue - State: closed - Opened by jlmaccal over 2 years ago - 3 comments
Labels: enhancement

#116 - setup single GPU

Issue - State: open - Opened by aspitaleri almost 3 years ago - 5 comments

#115 - Changes to comm.py for Issue #114

Pull Request - State: open - Opened by ca-taylor almost 3 years ago

#114 - SLURM 21.08.4 breaks MELD

Issue - State: open - Opened by ca-taylor almost 3 years ago - 10 comments

#113 - Meld 0.5.0: ModuleNotFoundError: No module named 'meld.system.meld_system'

Issue - State: closed - Opened by ca-taylor almost 3 years ago - 6 comments

#112 - Error: identifier "MAXFLOAT" is undefined

Issue - State: closed - Opened by ca-taylor almost 3 years ago - 7 comments

#111 - Add grid force

Pull Request - State: closed - Opened by ccccclw almost 3 years ago - 6 comments

#110 - Extend simulation length

Issue - State: open - Opened by ccccclw about 3 years ago

#109 - Optimize handling of peak mappings

Issue - State: open - Opened by jlmaccal about 3 years ago
Labels: enhancement

#108 - Optimize handling of groups and collections

Issue - State: closed - Opened by jlmaccal about 3 years ago
Labels: enhancement

#107 - Improved efficiency of mapper MC

Pull Request - State: closed - Opened by jlmaccal about 3 years ago

#106 - Add utility functions for secondary structure / torsions

Issue - State: open - Opened by jlmaccal about 3 years ago - 3 comments
Labels: enhancement

#105 - Question on restraint creation in the protein peptide tutorial

Issue - State: closed - Opened by proteins247 about 3 years ago - 2 comments

#104 - Scaled exponential

Pull Request - State: closed - Opened by jlmaccal about 3 years ago

#103 - Added bounds-checking to modification functions

Pull Request - State: closed - Opened by jlmaccal about 3 years ago

#102 - Export ScaledExponential

Pull Request - State: closed - Opened by jlmaccal about 3 years ago

#101 - Implement ScaledExponentialDiscretePrior

Pull Request - State: closed - Opened by jlmaccal about 3 years ago

#100 - edits to prepare_restart due to changes in vault.py

Pull Request - State: closed - Opened by kgaalswyk about 3 years ago

#99 - MELD tutorials

Pull Request - State: closed - Opened by arupmondal835 about 3 years ago - 2 comments

#98 - Fix slow minimization

Issue - State: open - Opened by jlmaccal about 3 years ago

#97 - Force field selection

Issue - State: open - Opened by alberto99 about 3 years ago - 3 comments
Labels: enhancement

#96 - Fixed unit conversion for RDC

Pull Request - State: closed - Opened by jlmaccal over 3 years ago

#95 - MELD Force direction issue in the reference platform

Issue - State: open - Opened by frank-stonybrook over 3 years ago - 18 comments

#94 - unit fix

Pull Request - State: closed - Opened by ccccclw over 3 years ago

#93 - PeakMapping use case

Issue - State: closed - Opened by frank-stonybrook over 3 years ago - 1 comment

#92 - Add error checking to Reference plugin

Issue - State: open - Opened by jlmaccal over 3 years ago
Labels: enhancement

#91 - Monte Carlo should be easier to setup

Issue - State: open - Opened by jlmaccal over 3 years ago
Labels: enhancement

#90 - Implement Bayesian parameter sampling

Pull Request - State: closed - Opened by jlmaccal over 3 years ago

#89 - Major code re-organization

Pull Request - State: closed - Opened by jlmaccal over 3 years ago - 1 comment

#88 - Update indexing

Pull Request - State: closed - Opened by jlmaccal over 3 years ago

#87 - Update to new indexing scheme

Pull Request - State: closed - Opened by jlmaccal over 3 years ago

#86 - Move AMAP to transformer

Issue - State: closed - Opened by jlmaccal over 3 years ago
Labels: enhancement

#85 - Fix negotiate_device_id

Pull Request - State: closed - Opened by jlmaccal over 3 years ago

#84 - MELD and CUDA_VISIBLE_DEVICES under SLURM

Issue - State: closed - Opened by ca-taylor over 3 years ago - 12 comments

#83 - Switch to nvidia's cub for collective operations

Pull Request - State: closed - Opened by jlmaccal over 3 years ago

#82 - Add reference implementation

Pull Request - State: closed - Opened by jlmaccal over 3 years ago

#81 - Added ramp scaling to Ez portion of energy in RDCRestraintTransformer

Pull Request - State: closed - Opened by splenz over 3 years ago

#80 - Switch logging back to fork

Pull Request - State: closed - Opened by jlmaccal over 3 years ago

#79 - Race condition affecting shut down

Issue - State: closed - Opened by jlmaccal over 3 years ago
Labels: bug

#77 - Likelihood accuracy parameter is a static prior

Issue - State: closed - Opened by alberto99 almost 4 years ago - 3 comments
Labels: enhancement

#76 - OpenMMSwigHeaders.i: Syntax Error

Issue - State: closed - Opened by ca-taylor about 4 years ago - 14 comments

#75 - Communication with mpi protocols

Issue - State: closed - Opened by alberto99 about 4 years ago - 16 comments

#74 - Fix `StopIteration` related error in comm.py

Pull Request - State: closed - Opened by jlmaccal about 4 years ago - 1 comment

#73 - Update Timeout

Pull Request - State: closed - Opened by jlmaccal about 4 years ago

#72 - comm.py communication issues with python3.7

Issue - State: closed - Opened by alberto99 about 4 years ago - 15 comments

#71 - Confusion about distance restraints under PBC

Issue - State: open - Opened by frank-stonybrook over 4 years ago - 17 comments

#70 - Remove master/slave terminology

Issue - State: closed - Opened by jlmaccal over 4 years ago
Labels: enhancement

#69 - Error launching MELD on nodes with multiple GPUs

Issue - State: closed - Opened by frank-stonybrook almost 5 years ago - 2 comments

#68 - Segmentation fault for large sequences

Issue - State: closed - Opened by eguzki about 5 years ago

#67 - Launch REMD error (platform error)

Issue - State: closed - Opened by zhenglz over 5 years ago - 1 comment

#66 - Change initial position of alignment tensor particles

Issue - State: open - Opened by jlmaccal over 5 years ago

#65 - Simulations don't die after crash

Issue - State: closed - Opened by jlmaccal over 5 years ago

#64 - Change scaler minimum values

Issue - State: closed - Opened by jlmaccal over 5 years ago

#63 - Implement new handing of RDCs

Pull Request - State: closed - Opened by jlmaccal over 5 years ago

#62 - CPU/Reference implementation of MELD restraints

Issue - State: closed - Opened by jchodera almost 6 years ago - 13 comments

#61 - conda install fails

Issue - State: closed - Opened by agrossfield almost 6 years ago - 4 comments

#59 - Issue with "Fix bug in handling of restraint groups"

Issue - State: closed - Opened by frank-stonybrook almost 6 years ago - 2 comments

#58 - MELD 0.4.7 not restartable from 0.4.6 runs

Issue - State: closed - Opened by cing almost 6 years ago - 1 comment

#57 - Added DCD export with box vectors

Pull Request - State: closed - Opened by cing almost 6 years ago

#56 - Box vectors are not written to DCD using "extract_trajectory"

Issue - State: closed - Opened by cing almost 6 years ago

#55 - Meld 0.3.10 compile against OpenMM 7.2.2 failed

Issue - State: closed - Opened by frank-stonybrook over 6 years ago - 1 comment

#51 - Add type hints

Issue - State: closed - Opened by jlmaccal over 6 years ago
Labels: enhancement

#50 - Finish removing osx support

Issue - State: closed - Opened by jlmaccal over 6 years ago
Labels: enhancement

#48 - Convert docstrings to numpydoc format

Issue - State: closed - Opened by jlmaccal over 6 years ago
Labels: help wanted

#47 - Fix documentation build and upload

Issue - State: closed - Opened by jlmaccal over 6 years ago - 1 comment
Labels: help wanted

#45 - Add unit tests for REST2 transformer

Issue - State: closed - Opened by jlmaccal over 6 years ago
Labels: enhancement