ur-whitelab/peptidesim issues and pull requests

#96 - Take .pdb file as initial structure input

Issue - State: open - Opened by hgandhi2411 over 3 years ago

#95 - test_pte fails

Issue - State: closed - Opened by navneeth3005 over 3 years ago - 1 comment

#94 - Added function to create shift_dict

Pull Request - State: open - Opened by hgandhi2411 almost 4 years ago - 1 comment
Labels: wip

#93 - Add utility function to create `shift_dict` from .dat files

Issue - State: open - Opened by hgandhi2411 almost 4 years ago

#92 - Added instructions on using any new forcefield

Pull Request - State: closed - Opened by hgandhi2411 about 4 years ago - 4 comments

#91 - Improve logging

Issue - State: closed - Opened by hgandhi2411 about 4 years ago - 1 comment
Labels: enhancement

#90 - Add This FF

Issue - State: closed - Opened by whitead over 4 years ago - 1 comment

#89 - Amidate and Acetylate End group support

Pull Request - State: closed - Opened by whitead over 4 years ago - 1 comment

#88 - WIP: Adding Crowders

Pull Request - State: open - Opened by whitead over 4 years ago - 1 comment
Labels: wip

#87 - V5 release

Pull Request - State: closed - Opened by whitead over 4 years ago

#86 - Density correction

Pull Request - State: closed - Opened by whitead over 4 years ago - 1 comment

#85 - Create ramachandran plotting code for trajectories

Pull Request - State: closed - Opened by whitead over 4 years ago - 1 comment

#84 - Remove traitlets

Issue - State: closed - Opened by whitead over 4 years ago

#83 - Added additional analysis code for pt-wte overlap and nmr cs

Pull Request - State: closed - Opened by whitead over 4 years ago - 1 comment

#82 - Added automatic cs2backbone plumed script generator

Pull Request - State: closed - Opened by whitead over 4 years ago - 1 comment

#81 - Fixed bugs in part_2.py in `inputs/abeta_sims/`

Pull Request - State: closed - Opened by hgandhi2411 over 4 years ago - 1 comment

#80 - Update input/abeta_sims/part2_long.py file

Issue - State: closed - Opened by hgandhi2411 over 4 years ago
Labels: bug

#79 - Cleaned-up files appearing in root and location of PTE hills

Pull Request - State: closed - Opened by whitead almost 5 years ago - 1 comment

#78 - Made test compatible with CS in plumed 2.6

Pull Request - State: closed - Opened by mehradans92 almost 5 years ago - 1 comment

#77 - get_replex_e attribute not being recognized.

Issue - State: closed - Opened by mchakra2 almost 5 years ago - 2 comments
Labels: bug

#76 - Fixed SameFileError in ps.add_file()

Pull Request - State: closed - Opened by hgandhi2411 almost 5 years ago - 1 comment

#75 - Issue 5

Pull Request - State: closed - Opened by mchakra2 almost 5 years ago - 1 comment

#74 - Added two methods for analyzing EDS restarts

Pull Request - State: closed - Opened by whitead almost 5 years ago - 4 comments

#73 - Update CS2Backbone Checker

Issue - State: closed - Opened by whitead almost 5 years ago

#72 - Check Plumed Version

Issue - State: closed - Opened by whitead almost 5 years ago

#71 - HILLS Files end up in root directory which is inconvienent

Issue - State: closed - Opened by whitead almost 5 years ago - 1 comment

#70 - Made signal handling more robust

Pull Request - State: closed - Opened by whitead almost 5 years ago - 1 comment

#69 - Weights metad

Pull Request - State: closed - Opened by dilnoza92 almost 5 years ago - 4 comments

#68 - Added a test for multiple restarts

Pull Request - State: closed - Opened by hgandhi2411 almost 5 years ago - 4 comments

#67 - Remove pickling from input scripts

Issue - State: closed - Opened by whitead almost 5 years ago - 1 comment

#66 - Remove pickling from input scripts

Issue - State: closed - Opened by whitead almost 5 years ago - 1 comment

#65 - Add check on success

Issue - State: closed - Opened by whitead almost 5 years ago - 1 comment

#64 - Metadynamics

Pull Request - State: closed - Opened by dilnoza92 almost 5 years ago - 1 comment

#63 - Separate bonded and non-bonded interactions using simulation rerun

Issue - State: open - Opened by mchakra2 almost 5 years ago

#62 - Report generation

Issue - State: closed - Opened by whitead almost 5 years ago - 1 comment
Labels: enhancement

#61 - Made simulation names depend on mdp keywords and filename

Pull Request - State: closed - Opened by whitead almost 5 years ago

#60 - Grompp error on restart if previous pickle files are not deleted

Issue - State: closed - Opened by hgandhi2411 almost 5 years ago - 2 comments

#59 - MDP kwargs don't change on restart

Issue - State: closed - Opened by hgandhi2411 almost 5 years ago - 1 comment

#58 - Generating weights file after running metadynamics

Issue - State: closed - Opened by dilnoza92 almost 5 years ago - 1 comment

#57 - Made forces output by default for NVT

Pull Request - State: closed - Opened by whitead almost 5 years ago

#56 - WIP: Function to modify gromacs PDB to have unique chain IDs

Pull Request - State: closed - Opened by hgandhi2411 almost 5 years ago - 7 comments

#55 - Handle multiple peptide sequences well

Issue - State: closed - Opened by hgandhi2411 almost 5 years ago - 4 comments

#54 - Fixed CA and CB invalid cs_shift values

Pull Request - State: closed - Opened by mehradans92 almost 5 years ago - 2 comments

#53 - Removes leftover files from tests

Pull Request - State: closed - Opened by hgandhi2411 almost 5 years ago - 5 comments

#52 - Remove files created from tests

Issue - State: closed - Opened by hgandhi2411 almost 5 years ago - 4 comments

#51 - Peptidesim Tutorial on jupyter notebook

Pull Request - State: closed - Opened by dilnoza92 almost 5 years ago

#50 - Test Failure in Peptidesim

Issue - State: closed - Opened by whitead almost 5 years ago - 2 comments
Labels: bug

#49 - Removed extra trr files floating around

Pull Request - State: closed - Opened by whitead almost 5 years ago

#48 - Output forces for all simulations by default

Issue - State: closed - Opened by hgandhi2411 almost 5 years ago - 1 comment

#47 - README Improvements

Issue - State: closed - Opened by whitead almost 5 years ago - 1 comment

#46 - WIP: Made it faster to run peptidesim tests

Pull Request - State: closed - Opened by whitead almost 5 years ago - 1 comment

#46 - WIP: Made it faster to run peptidesim tests

Pull Request - State: closed - Opened by whitead almost 5 years ago - 1 comment

#45 - Speed-up Tests

Issue - State: closed - Opened by whitead almost 5 years ago - 1 comment

#45 - Speed-up Tests

Issue - State: closed - Opened by whitead almost 5 years ago - 1 comment

#44 - PTE update

Pull Request - State: closed - Opened by JinyuXu almost 5 years ago

#43 - Added automatic save/load from pickle files

Pull Request - State: closed - Opened by whitead almost 5 years ago - 2 comments

#42 - Added README TOC and Changelog

Pull Request - State: closed - Opened by whitead almost 5 years ago

#41 - Have peptidesim object handle pickling

Issue - State: closed - Opened by whitead almost 5 years ago - 1 comment

#41 - Have peptidesim object handle pickling

Issue - State: closed - Opened by whitead almost 5 years ago - 1 comment

#40 - Add release notes

Issue - State: closed - Opened by whitead almost 5 years ago

#39 - renamed test file to start with test_

Pull Request - State: closed - Opened by whitead almost 5 years ago

#38 - Updated to latest peptidebuilder version that fixes biopython imports

Pull Request - State: closed - Opened by whitead almost 5 years ago - 3 comments

#37 - added the python inputs to run abeta simulations with new installation

Pull Request - State: closed - Opened by dilnoza92 almost 5 years ago - 4 comments

#37 - added the python inputs to run abeta simulations with new installation

Pull Request - State: closed - Opened by dilnoza92 almost 5 years ago - 4 comments

#36 - fixed add_file not updating plumed file and added tests for them

Pull Request - State: closed - Opened by dilnoza92 almost 5 years ago - 3 comments

#35 - CI and add to PR checks

Issue - State: closed - Opened by whitead almost 5 years ago - 1 comment

#34 - rename test file

Issue - State: closed - Opened by whitead almost 5 years ago - 1 comment

#33 - Documentation update

Pull Request - State: closed - Opened by JinyuXu almost 5 years ago - 3 comments

#32 - Unittest added for asserting the chemical shifts

Pull Request - State: closed - Opened by mehradans92 almost 5 years ago - 13 comments

#31 - read_me

Pull Request - State: closed - Opened by dilnoza92 almost 5 years ago

#30 - Readme

Pull Request - State: closed - Opened by dilnoza92 almost 5 years ago - 1 comment

#29 - Updatereadme

Pull Request - State: closed - Opened by dilnoza92 almost 5 years ago - 1 comment

#28 - Add doc for running tests on bluehive (incl clean-up)

Issue - State: closed - Opened by whitead almost 5 years ago - 1 comment

#27 - Converted input scripts from python 2 to 3

Pull Request - State: closed - Opened by mchakra2 almost 5 years ago - 3 comments

#26 - Updated the README to work with new gromacs version

Pull Request - State: closed - Opened by dilnoza92 about 5 years ago - 2 comments

#25 - Issue/24

Pull Request - State: closed - Opened by dilnoza92 about 5 years ago - 5 comments

#24 - add_file() function is not modifying already existing files in the local directories.

Issue - State: closed - Opened by dilnoza92 about 5 years ago - 3 comments

#23 - Hashing uses top file

Issue - State: closed - Opened by whitead about 5 years ago - 2 comments

#22 - Converting python2 to python3

Issue - State: closed - Opened by dilnoza92 about 5 years ago - 1 comment

#21 - Fix upstream peptidebuilder biopython issue

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

#20 - Gromacs 2019 no longer supports mdrun multi

Issue - State: closed - Opened by whitead about 5 years ago - 1 comment

#19 - New Testing Env for Python3

Pull Request - State: closed - Opened by whitead about 5 years ago - 2 comments

#18 - Printing Peptide Object

Issue - State: closed - Opened by whitead about 5 years ago - 3 comments
Labels: enhancement

#17 - Update docker images

Issue - State: closed - Opened by whitead about 5 years ago - 1 comment

#16 - Update README.md

Pull Request - State: closed - Opened by JinyuXu about 5 years ago

#15 - Non source documentation

Issue - State: closed - Opened by whitead about 5 years ago - 1 comment

#14 - Plotting code for diagnostics

Issue - State: closed - Opened by whitead about 5 years ago - 1 comment
Labels: enhancement

#13 - Non-aqueous solvent in gromacs

Issue - State: closed - Opened by whitead about 5 years ago - 1 comment
Labels: enhancement

#12 - Make metadynamics template file for enhanced sampling

Issue - State: closed - Opened by whitead about 5 years ago - 1 comment

#11 - Changing gromacs generated PDB chains to work for plumed

Issue - State: closed - Opened by whitead about 5 years ago - 1 comment

#11 - Changing gromacs generated PDB chains to work for plumed

Issue - State: closed - Opened by whitead about 5 years ago - 1 comment

#10 - Assert all experimental shifts exist

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

#9 - Be more intelligent about bias limits and detect blow ups

Issue - State: closed - Opened by whitead about 5 years ago - 1 comment

#8 - EDS Bias restarts past more than 2 fails

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

#7 - Replica exchange tuning is fragile

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

#6 - PTE tuning log file not found

Issue - State: closed - Opened by whitead about 5 years ago - 2 comments

#5 - Remove files when removing items from pickle object

Issue - State: closed - Opened by whitead about 5 years ago - 4 comments
Labels: enhancement

GitHub / ur-whitelab/peptidesim issues and pull requests