Ecosyste.ms: Issues

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GitHub / shirtsgroup/InterMol issues and pull requests

#401 - Gromacs topology parser

Issue - State: open - Opened by subhamoymahajan 4 months ago

#400 - trjconv-error in input

Issue - State: open - Opened by prisi20183 5 months ago

#399 - LAMMPS TO GROMACS CONVERSION

Issue - State: open - Opened by prisi20183 6 months ago

#397 - IndexError: list index out of range

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

#396 - Fix: LAMMPS to Gromacs Conversion Issues

Pull Request - State: open - Opened by Jeet-Majumdar over 1 year ago

#395 - convert lammps to gromacs (error about dihedral)

Issue - State: open - Opened by Springwonder over 1 year ago - 7 comments

#393 - Gromacs to AMBER ligand conversion

Issue - State: open - Opened by mmagithub almost 2 years ago - 6 comments

#392 - LAMMPS to Gromacs conversion errors

Issue - State: open - Opened by MM2023-1401 almost 2 years ago - 4 comments

#391 - Add versioneer as a build-time dependency

Pull Request - State: open - Opened by mattwthompson about 2 years ago

#390 - Add long_description_content_type

Pull Request - State: open - Opened by Gerardwx about 2 years ago - 1 comment

#389 - Update package setup

Pull Request - State: closed - Opened by mattwthompson about 2 years ago - 1 comment

#388 - SyntaxError: invalid syntax

Issue - State: open - Opened by debanjansen48 over 2 years ago - 1 comment

#387 - Lammps to Gromacs: Include Cvff Improper Style and OPLS dihedral

Pull Request - State: closed - Opened by Jeet-Majumdar over 2 years ago - 5 comments

#386 - Update CI to use Python 3.8 through 3.10

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

#385 - issue with import intermol.gromacs .... SyntaxError

Issue - State: open - Opened by kishantchem over 2 years ago - 1 comment

#384 - Update convert.py

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

#383 - Issue when converting from Desmond input to LAMMPS output

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

#382 - Dihedral error converting from Desmond to Gromacs

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

#381 - Problem to start Intermol

Issue - State: open - Opened by kleflick about 3 years ago - 1 comment

#380 - Import directly from six

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

#379 - Lammps parser fix

Pull Request - State: open - Opened by orionarcher over 3 years ago - 12 comments

#378 - Several bugs in Lammps IO

Issue - State: closed - Opened by orionarcher over 3 years ago - 4 comments

#377 - Issue with parmed.utils.six

Issue - State: closed - Opened by samuele-giannini over 3 years ago - 5 comments

#376 - Error Converting Gromacs to Lammps

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

#375 - Update collections imports for deprecations

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

#374 - Error in converting cms file of a ligand with pseudoatom

Issue - State: open - Opened by amrhamedp about 4 years ago - 3 comments

#373 - Add convert.py alias to $PATH

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

#372 - Error in converting cms to Gromacs topology

Issue - State: open - Opened by Moh-Pou about 4 years ago - 1 comment

#371 - Update setup-miniconda action, setup.py version

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

#370 - Add Python 3.8 and 3.9 to CI

Pull Request - State: closed - Opened by mattwthompson over 4 years ago - 2 comments

#369 - Distribute on conda-forge

Issue - State: closed - Opened by mattwthompson over 4 years ago - 2 comments

#368 - Units from GROMACS to LAMMPS

Issue - State: open - Opened by moradza over 4 years ago - 1 comment

#367 - Set up GitHub Actions CI

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

#366 - Update Python versions in CI

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

#365 - Conversion DESMOND--> AMBER

Issue - State: open - Opened by icamps over 4 years ago - 5 comments

#364 - Converting from Amber to LAMMPS with flexible water

Issue - State: open - Opened by nickhine over 4 years ago - 6 comments

#362 - Error converting amber file

Issue - State: closed - Opened by askusay over 4 years ago - 4 comments

#361 - input files for testing the energy conservation between amber and gromacs

Issue - State: closed - Opened by xiki-tempula about 5 years ago - 5 comments

#360 - IndexError: index 8 is out of bounds for axis 1 with size 8

Issue - State: closed - Opened by skblnw over 5 years ago - 3 comments

#359 - Desmond to Prmtop

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

#358 - Bugfixes

Pull Request - State: closed - Opened by mrshirts over 5 years ago - 2 comments

#357 - Tilt factors ignored when converting from GROMACS to LAMMPS

Issue - State: closed - Opened by nabraham47 over 5 years ago - 3 comments

#356 - LJ Recip not included in Gromacs Energy Comparison

Issue - State: closed - Opened by nabraham47 over 5 years ago

#355 - InterMol does not recognize coeff keywords in the lammps input files

Issue - State: open - Opened by JoshuaSBrown almost 6 years ago - 2 comments

#353 - OpenMM to Gromacs by using InterMol

Issue - State: open - Opened by nividic about 6 years ago - 3 comments

#352 - UnboundLocalError: local variable 'npermol' referenced before assignment

Issue - State: open - Opened by phenylazide about 6 years ago - 1 comment

#351 - Desmond to gromacs nrexcl 0 warning

Issue - State: open - Opened by sirishkaushik over 6 years ago

#349 - Set coefficients to 0 if they were missing from input file, this is a…

Pull Request - State: open - Opened by JoshuaSBrown over 6 years ago - 4 comments

#348 - Reading Lammps data files (Number of Dihedral Coefficients gives errors)

Issue - State: open - Opened by JoshuaSBrown over 6 years ago - 3 comments

#347 - Addressed error with dimension and boundary keywords

Pull Request - State: closed - Opened by JoshuaSBrown over 6 years ago - 1 comment

#346 - Bug - in lammps parser caused from using a dict

Issue - State: closed - Opened by JoshuaSBrown over 6 years ago - 6 comments

#344 - Desmond conversion

Issue - State: open - Opened by tjgdamen almost 7 years ago - 6 comments

#343 - DLPOLY maybe?

Issue - State: open - Opened by sperezconesa about 7 years ago - 1 comment
Labels: feature

#342 - Possible bug in GMX2LAMMPS energy evaluation with waters.

Issue - State: open - Opened by sperezconesa about 7 years ago - 1 comment
Labels: LAMMPS, GROMACS

#341 - Desmond to GMX

Issue - State: open - Opened by billy-noonan over 7 years ago - 4 comments

#340 - Issues with installing InterMol

Issue - State: open - Opened by yinglongmiao over 7 years ago - 19 comments

#339 - Removing time bottlenecks for Desmond parsing

Issue - State: open - Opened by mrshirts over 7 years ago - 6 comments
Labels: DESMOND

#338 - Fix for .gro file output with too many atoms.

Pull Request - State: closed - Opened by mrshirts over 7 years ago

#337 - Desmond to gromacs conversion failing to parse quoted string

Issue - State: open - Opened by sup27606 over 7 years ago - 15 comments

#336 - sum_parameters?

Issue - State: open - Opened by mrshirts over 7 years ago - 4 comments
Labels: question

#335 - constraint fixes + fix for amber boxes

Pull Request - State: closed - Opened by mrshirts over 7 years ago

#334 - Updating changes implemented in the freesolv exercise

Pull Request - State: closed - Opened by mrshirts over 7 years ago

#333 - Desmond to gromacs

Issue - State: open - Opened by Dileepvijayan over 7 years ago - 2 comments

#332 - Amber to Desmond

Issue - State: closed - Opened by yiannisgaldadas over 7 years ago - 4 comments

#331 - Lammps errors with default parameters

Issue - State: open - Opened by mrshirts almost 8 years ago

#330 - Conversion from Desmond cms to Gromacs

Issue - State: open - Opened by yingyang90 almost 8 years ago - 11 comments

#329 - Add an option to specify the output units

Issue - State: open - Opened by maaren almost 8 years ago - 2 comments

#328 - replaced simtk.unit with parmed.unit

Pull Request - State: closed - Opened by maaren almost 8 years ago - 1 comment

#327 - Handle comparison of inputs of Amber files without box size

Issue - State: open - Opened by mrshirts almost 8 years ago
Labels: feature

#326 - mismatch in imported module name and name used.

Pull Request - State: closed - Opened by mrshirts almost 8 years ago

#325 - Use the ParmEd units module, instead of OpenMM

Issue - State: closed - Opened by mrshirts almost 8 years ago - 1 comment
Labels: feature

#324 - Only raise error for missing LAMMPS when called

Pull Request - State: closed - Opened by ctk3b almost 8 years ago - 12 comments

#323 - Have other codes call CHARMM when running unit tests.

Issue - State: open - Opened by mrshirts almost 8 years ago
Labels: testing

#322 - Add CHARMM as an input file for testing.

Issue - State: open - Opened by mrshirts almost 8 years ago
Labels: testing

#321 - Can't specify different binaries for testing

Issue - State: open - Opened by mrshirts almost 8 years ago
Labels: feature, testing

#320 - Address issues raised by Xubo lin with incorrect conversion to desmond

Issue - State: closed - Opened by mrshirts almost 8 years ago - 2 comments
Labels: DESMOND

#319 - Ensure that dihedraltype matching exactly matches gromacs logic

Issue - State: open - Opened by ctk3b almost 8 years ago
Labels: GROMACS

#318 - LAMMPS dihedral_style multi/harmonic coefficients mismatch

Issue - State: open - Opened by b-v almost 8 years ago - 4 comments
Labels: LAMMPS

#317 - Only complain about lammps binary not found if it is needed.

Issue - State: closed - Opened by mrshirts almost 8 years ago
Labels: LAMMPS

#316 - newlines in the -ls option are not passed through (#315)

Pull Request - State: closed - Opened by maaren almost 8 years ago - 1 comment

#315 - newlines in the -ls option are not passed through

Issue - State: closed - Opened by maaren almost 8 years ago - 2 comments

#314 - Pairtypes are missing in the generated lammps input

Issue - State: open - Opened by maaren almost 8 years ago - 1 comment
Labels: bug, LAMMPS

#313 - reorder atom_orders starting from best match (#312)

Pull Request - State: closed - Opened by maaren about 8 years ago - 3 comments

#312 - InterMol selecting the last match for dihedrals?

Issue - State: closed - Opened by mrshirts about 8 years ago - 5 comments
Labels: GROMACS

#311 - Merging/increasing compatibility with ParmEd

Issue - State: open - Opened by ctk3b about 8 years ago - 2 comments

#310 - Multiple entries for same molecule type in [ molecules ] break G->L conversion

Issue - State: open - Opened by ctk3b about 8 years ago - 5 comments
Labels: bug, LAMMPS

#309 - GROMACS dihedraltype lookup appears to choose first successful lookup

Issue - State: closed - Opened by ctk3b about 8 years ago - 2 comments
Labels: bug, GROMACS

#308 - Simplify energy grouping accross simulators

Pull Request - State: closed - Opened by ctk3b about 8 years ago - 18 comments

#307 - Correctly group non-bonded energies in output

Pull Request - State: closed - Opened by ctk3b about 8 years ago

#306 - Remove upper limit on # atoms in LAMMPS forces

Pull Request - State: closed - Opened by ctk3b about 8 years ago

#305 - Print LAMMPS UB angles as float

Pull Request - State: closed - Opened by ctk3b about 8 years ago

#304 - [WIP] fix for writing of virtuals in Desmond

Pull Request - State: open - Opened by mrshirts about 8 years ago - 1 comment

#297 - Exclusion handling for 4 site water is not doing G->D correctly.

Issue - State: open - Opened by mrshirts about 8 years ago
Labels: DESMOND

#294 - no atom names in dms file

Issue - State: open - Opened by Marcela51 about 8 years ago - 2 comments
Labels: DESMOND