Ecosyste.ms: Issues

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GitHub / fhh2626/BFEE2 issues and pull requests

#134 - membrane proteins

Issue - State: open - Opened by amara86 3 months ago - 1 comment

#132 - Dev

Pull Request - State: closed - Opened by fhh2626 5 months ago

#130 - Alchemical calculations for charged ligands

Issue - State: open - Opened by ballaneypranav 6 months ago - 1 comment

#129 - Unable to open extended system file

Issue - State: closed - Opened by kehan777 6 months ago - 1 comment

#128 - ERROR in Post-treatment

Issue - State: open - Opened by STM32F103C8T6 6 months ago - 2 comments

#127 - Supplementary Data acquisition

Issue - State: closed - Opened by ljh433 6 months ago - 4 comments

#126 - sh: 15: hash: Illegal option -t

Issue - State: closed - Opened by ljh433 6 months ago - 2 comments

#125 - Update environment

Pull Request - State: closed - Opened by Tinkbian 7 months ago

#124 - Tinkbian q6

Pull Request - State: closed - Opened by Tinkbian 7 months ago - 3 comments

#123 - Update gui.py

Pull Request - State: closed - Opened by Tinkbian 7 months ago

#122 - rebase

Pull Request - State: closed - Opened by fhh2626 9 months ago

#121 - Mistakes with the tempetarute targets

Issue - State: open - Opened by groponp 9 months ago - 4 comments

#118 - colvars2.in does not exist!

Issue - State: closed - Opened by shradheyagupta 11 months ago - 1 comment

#115 - FATAL ERROR: CUDA error in ComputeBondedCUDA

Issue - State: closed - Opened by shradheyagupta 11 months ago - 1 comment

#113 - version 2.5.0 updates

Pull Request - State: closed - Opened by fhh2626 11 months ago

#112 - rebase

Pull Request - State: closed - Opened by fhh2626 11 months ago

#111 - Which parameter files to include in BFEE2?

Issue - State: closed - Opened by th-of 11 months ago

#110 - Can a small DNA fragment be considered a ligand in BFEE

Issue - State: open - Opened by yasirmamun2088 about 1 year ago - 5 comments

#109 - error when distributing on PyPI

Issue - State: closed - Opened by fhh2626 over 1 year ago - 3 comments

#108 - update version to 2.4.1

Pull Request - State: closed - Opened by fhh2626 over 1 year ago

#107 - Update configTemplate.py

Pull Request - State: closed - Opened by fhh2626 over 1 year ago

#106 - BFEE2Gui window Error after Procedure 1, Step 6

Issue - State: closed - Opened by mglgc over 1 year ago - 15 comments

#105 - Error with BFEE2Gui Generate Inputs button

Issue - State: closed - Opened by mglgc over 1 year ago - 3 comments

#104 - merge dev to main

Pull Request - State: closed - Opened by fhh2626 over 1 year ago

#103 - Error in Step 007 `Jacobi`

Issue - State: closed - Opened by groponp over 1 year ago - 9 comments

#102 - Use python module

Issue - State: open - Opened by groponp over 1 year ago - 1 comment

#101 - rebase main

Pull Request - State: closed - Opened by fhh2626 over 1 year ago

#100 - Add SOL residue name to water selection for Gromacs

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

#99 - Problem with box size

Issue - State: open - Opened by groponp over 1 year ago - 2 comments

#98 - Question: update centers

Issue - State: closed - Opened by ReneHamburger1993 almost 2 years ago - 3 comments

#97 - GROMACS: Use Parrinello-Rahman barostat

Pull Request - State: closed - Opened by HanatoK almost 2 years ago - 14 comments

#96 - Unknown error! Could not convert string "if" to float64 at row 0, colum 1

Issue - State: open - Opened by Tangbbmc almost 2 years ago - 10 comments

#95 - Installation of BFEE2 with conda failed.

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

#94 - version 2.3.2

Pull Request - State: closed - Opened by fhh2626 almost 2 years ago

#93 - forceconstant values for free energy calculations

Issue - State: closed - Opened by ndonyapour almost 2 years ago - 4 comments

#92 - Asking BFEE2

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

#91 - How make stratification?

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

#90 - rebase

Pull Request - State: closed - Opened by fhh2626 almost 2 years ago

#89 - Dev

Pull Request - State: closed - Opened by fhh2626 about 2 years ago

#88 - AssertionError in PostTreatment - gromacs run

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

#87 - OPLS Implementation?

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

#86 - NAMD 3.0

Issue - State: open - Opened by bhavranek over 2 years ago - 2 comments

#85 - How to Install BFEE2 VMD Plugin?

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

#84 - suggestions on GPU usage

Issue - State: closed - Opened by Blockbastermaker over 2 years ago

#83 - rebase

Pull Request - State: closed - Opened by fhh2626 over 2 years ago

#82 - merge Dev branch

Pull Request - State: closed - Opened by fhh2626 over 2 years ago

#81 - rebase main branch

Pull Request - State: closed - Opened by fhh2626 almost 3 years ago

#78 - Should water be included in the psf and pdb that needs to be uploaded?

Issue - State: closed - Opened by bhavranek almost 3 years ago - 1 comment

#77 - Error in the colvars module

Issue - State: closed - Opened by almeida85 almost 3 years ago - 2 comments

#76 - BFEE2 tutorial

Issue - State: closed - Opened by almeida85 almost 3 years ago - 1 comment

#75 - merge dev branch

Pull Request - State: closed - Opened by fhh2626 almost 3 years ago

#74 - Fix alchemical stratification of step 3

Pull Request - State: closed - Opened by fhh2626 over 3 years ago

#73 - Replace posixpath.abspath/relpath to os.path.abspath/relpath

Pull Request - State: closed - Opened by fhh2626 over 3 years ago - 2 comments

#72 - ERROR: Constraint failure in RATTLE algorithm for atom 2572!

Issue - State: open - Opened by bhavranek over 3 years ago - 3 comments

#71 - use os.path to replace posixpath

Pull Request - State: closed - Opened by fhh2626 over 3 years ago - 2 comments

#70 - BFEEGromacs does not work under Windows 11

Issue - State: closed - Opened by fhh2626 over 3 years ago - 7 comments

#69 - Merge dev branch

Pull Request - State: closed - Opened by fhh2626 over 3 years ago

#68 - Fix the wrong estimation of r

Pull Request - State: closed - Opened by fhh2626 over 3 years ago - 1 comment

#67 - differences in NAMD and GROMACS setups

Issue - State: closed - Opened by ReneHamburger1993 over 3 years ago - 2 comments

#66 - HINT/command for output redirection missing?

Issue - State: closed - Opened by ReneHamburger1993 over 3 years ago - 2 comments

#65 - merge dev branch

Pull Request - State: closed - Opened by fhh2626 over 3 years ago

#64 - rebase from main

Pull Request - State: closed - Opened by fhh2626 over 3 years ago

#63 - merge Dev branch

Pull Request - State: closed - Opened by fhh2626 over 3 years ago

#62 - new definition of polar angles

Pull Request - State: closed - Opened by fhh2626 over 3 years ago

#61 - implemented new CVs

Pull Request - State: closed - Opened by fhh2626 over 3 years ago

#60 - Error in selection

Issue - State: open - Opened by gokulalgates over 3 years ago - 5 comments

#59 - Fix copying of gmx force field files and allow non-standard PDB.

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

#58 - merge Dev branch

Pull Request - State: closed - Opened by fhh2626 over 3 years ago

#57 - Use centerToOrigin for euler and polar angles.

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

#56 - BFEE VMD Plugin

Issue - State: open - Opened by bhavranek over 3 years ago - 2 comments

#55 - merge changes from Dev

Pull Request - State: closed - Opened by fhh2626 over 3 years ago

#54 - (WIP) initial try of using sphinx generate API doc

Pull Request - State: closed - Opened by fhh2626 over 3 years ago - 4 comments

#53 - Cumulative update from Dev

Pull Request - State: closed - Opened by fhh2626 over 3 years ago

#52 - Fix file dialogs.

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

#51 - move files to restructure the code

Pull Request - State: closed - Opened by fhh2626 over 3 years ago - 1 comment

#50 - version 2.1.7

Pull Request - State: closed - Opened by fhh2626 over 3 years ago

#49 - adapt mac menubar

Pull Request - State: closed - Opened by fhh2626 over 3 years ago

#48 - merge Dev branch

Pull Request - State: closed - Opened by fhh2626 over 3 years ago

#47 - Remove circular dependency of the setup.py.

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

#46 - Merge dev to main

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

#45 - Separate the version string into a standalone file and bump it to 2.1.4.

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

#44 - rebase main

Pull Request - State: closed - Opened by fhh2626 over 3 years ago

#43 - merge dev branch

Pull Request - State: closed - Opened by fhh2626 over 3 years ago

#42 - Test about cross-platform ability of BFEE2

Issue - State: closed - Opened by fhh2626 over 3 years ago - 12 comments

#41 - Fix open doc via browser

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

#40 - Remove include_package_data and bug fix for empty lists.

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

#39 - merge Dev branch

Pull Request - State: closed - Opened by fhh2626 over 3 years ago

#38 - TODO list

Issue - State: closed - Opened by fhh2626 over 3 years ago

#37 - merge Dev branch

Pull Request - State: closed - Opened by fhh2626 over 3 years ago

#36 - Fix the generation of 002.colvars.dat.

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

#35 - Make BFEE2Gui.py executable.

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

#34 - Use sphinx to generate documents automatically.

Pull Request - State: closed - Opened by HanatoK over 3 years ago - 4 comments

#33 - test before first release

Issue - State: closed - Opened by fhh2626 almost 4 years ago - 1 comment