maccallumlab/meld issues and pull requests

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

Issue - State: open - Opened by damax34 11 months ago

#150 - Select model feature in process_density_map script

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

#149 - error while running launch_remd

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

#148 - Suggestion : Add nucleotide forcefields to parser - OL3 for RNA and DNA.OL15 for DNA

Issue - State: open - Opened by yoavatsmonraz about 1 year ago - 4 comments

#147 - trying to use cryofold 2 - "RuntimeError: Unknown scaler type "linear_blur"

Issue - State: open - Opened by yoavatsmonraz about 1 year ago - 1 comment

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

Pull Request - State: closed - Opened by ccccclw about 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 over 1 year ago - 2 comments

#138 - Implemented support for martini builder; fixed velocity initialization bug; convience changes to build_elastic_network_restraints.py

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

#137 - Implemented RDCs on CUDA and improved parameter sampling

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

#136 - Improve mapper sampling

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

#135 - Improve peak map sampling

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

#134 - Implement Martini builder

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

#133 - Issue Running MELD

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

#132 - Add support to generate velocities

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

#131 - Compile issues, on all OSs.

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

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

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

#129 - Changed CustomAngleForce function to sin^2(theta) from sqrt(sin(theta)) for stability reasons

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

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

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

#127 - Changed creation of virtual spin labels

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

#126 - Added freeze_atoms and remove_potential

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

#125 - Decoupled number of replicas from number of processes

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

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

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

#123 - Fixed force --> newforce bug and changed initial positioning of spin label particle

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

#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 over 2 years ago - 5 comments

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

Pull Request - State: open - Opened by ca-taylor over 2 years ago

#114 - SLURM 21.08.4 breaks MELD

Issue - State: open - Opened by ca-taylor over 2 years ago - 10 comments

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

Issue - State: closed - Opened by ca-taylor over 2 years ago - 6 comments

#112 - Error: identifier "MAXFLOAT" is undefined

Issue - State: closed - Opened by ca-taylor over 2 years ago - 7 comments

#111 - Add grid force

Pull Request - State: closed - Opened by ccccclw over 2 years ago - 6 comments

#110 - Extend simulation length

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

#109 - Optimize handling of peak mappings

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

#108 - Optimize handling of groups and collections

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

#107 - Improved efficiency of mapper MC

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

#106 - Add utility functions for secondary structure / torsions

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

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

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

#104 - Scaled exponential

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

#103 - Added bounds-checking to modification functions

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

#102 - Export ScaledExponential

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

#101 - Implement ScaledExponentialDiscretePrior

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

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

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

#99 - MELD tutorials

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

#98 - Fix slow minimization

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

#97 - Force field selection

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

#96 - Fixed unit conversion for RDC

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

#95 - MELD Force direction issue in the reference platform

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

#94 - unit fix

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

#93 - PeakMapping use case

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

#92 - Add error checking to Reference plugin

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