Ecosyste.ms: Issues

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GitHub / openmm/openmm issues and pull requests

#4069 - Unit compatibility bug?

Issue - State: closed - Opened by lvotapka over 1 year ago - 2 comments

#4068 - system.remove forces does not work

Issue - State: closed - Opened by dspoel over 1 year ago - 2 comments

#4067 - Question about neighbor list pair fetching from CUDA platform

Issue - State: open - Opened by dingye18 over 1 year ago - 8 comments
Labels: question

#4066 - Store bounding box sizes in half precision

Pull Request - State: closed - Opened by peastman over 1 year ago - 16 comments

#4065 - Maximizing ns/day for small systems

Issue - State: open - Opened by philipturner over 1 year ago - 20 comments

#4063 - O(n^2) scaling at several million atoms

Issue - State: open - Opened by philipturner over 1 year ago - 23 comments

#4062 - Energies between groups of atoms

Issue - State: open - Opened by tanmoy7989 over 1 year ago - 2 comments
Labels: question

#4061 - Fixed an incorrectly sized array

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

#4060 - Faster implementation of CustomHbondForce

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

#4059 - unsupported operand error

Issue - State: closed - Opened by OkKakao over 1 year ago - 1 comment

#4057 - Does openmm support forcefield like UFF?

Issue - State: closed - Opened by OkKakao over 1 year ago - 2 comments

#4056 - Particle positions have not been set

Issue - State: closed - Opened by H-EKE over 1 year ago - 4 comments

#4055 - Minimization gave broken residues

Issue - State: open - Opened by slweng0321 over 1 year ago - 10 comments

#4054 - Use more efficient version of updateContextState()

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

#4053 - Nonpolar solvation energy in OpenMM Implicit Solvent models

Issue - State: closed - Opened by membiophys over 1 year ago - 5 comments

#4052 - Static volume using MonteCarloMembraneBarostat

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

#4051 - Ways to optimize memory usage for large simulations?

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

#4050 - Barostat and immobile (mass zero) particles

Issue - State: closed - Opened by aizvorski over 1 year ago - 2 comments
Labels: question

#4049 - Fixed error in barostats

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

#4048 - Metadynamics implementation

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

#4047 - LRC not converging in CustomNonbondedForce

Issue - State: closed - Opened by aehogan over 1 year ago - 2 comments
Labels: question

#4046 - implicit solvent with pbc condition?

Issue - State: closed - Opened by slweng0321 over 1 year ago - 4 comments

#4045 - 'END' not consistent with common PDB record type

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

#4044 - Calculating Linear Interaction Energy

Issue - State: open - Opened by theDanMeister over 1 year ago - 6 comments
Labels: question, cookbook

#4043 - Fixed uninitialized memory error

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

#4042 - Cost of CustomHbondForce

Issue - State: closed - Opened by wayuer19 over 1 year ago - 17 comments
Labels: question

#4041 - Compiling openmm-8.0.0 from source

Issue - State: closed - Opened by daipayans over 1 year ago - 14 comments

#4040 - Integrate Alchemical Transfer Method (ATM) plugin into OpenMM main?

Issue - State: closed - Opened by jchodera over 1 year ago - 41 comments
Labels: enhancement

#4039 - CUDA_ERROR_ILLEGAL_ADDRESS (700) when trying multiple GPUs with Amoeba

Issue - State: open - Opened by andrewsb8 over 1 year ago - 6 comments

#4038 - Non-deterministic execution order in CustomIntegrator

Issue - State: closed - Opened by tristanic over 1 year ago - 8 comments
Labels: bug

#4037 - Computing rbias on-the-fly for metadynamics

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

#4036 - Error with CustomCVForce when running simulation on multiple GPUs

Issue - State: closed - Opened by ndonyapour over 1 year ago - 2 comments

#4035 - Check units for LocalEnergyMinimizer.minimize()

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

#4034 - Prevent molecules from accidentally getting wrapped by barostat

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

#4033 - CharmmParameterSet generator unpacking

Issue - State: closed - Opened by pipitoludovico over 1 year ago - 21 comments

#4032 - MonteCarloBarostat reimages molecules

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

#4031 - No template for NME, closest match is NME

Issue - State: closed - Opened by andrewsb8 over 1 year ago - 2 comments

#4030 - modulation blew up after sometime

Issue - State: open - Opened by suice07 over 1 year ago - 12 comments

#4029 - Ignore changes to force group after context creation

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

#4028 - Support GROMACS files that use GROMOS force fields

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

#4027 - amoebapme crash on Ubuntu 20.04.06

Issue - State: closed - Opened by bdenhollander over 1 year ago - 5 comments

#4026 - conda-forge openmm_dev channel is missing Python 3.11

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

#4025 - addMembrane() works with CustomNonbondedForce

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

#4024 - Missing patches in Amoeba force fields

Issue - State: closed - Opened by andrewsb8 over 1 year ago - 2 comments

#4023 - Problem adding membrane to system

Issue - State: closed - Opened by H-EKE over 1 year ago - 8 comments
Labels: bug

#4022 - No dimensionality checking is done for LocalEnergyMinimizer.minimize tolerance

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

#4021 - Protein flying away when using MonteCarloBarostat

Issue - State: open - Opened by asiomchen over 1 year ago - 4 comments

#4020 - DCD box size lost during warming up, but recovered later

Issue - State: closed - Opened by pipitoludovico over 1 year ago - 7 comments

#4019 - Expose constants via Python wrapper?

Issue - State: open - Opened by jchodera over 1 year ago - 3 comments
Labels: enhancement

#4018 - Defining Multiple CustomGBForces

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

#4017 - Metadynamics on custom CV

Issue - State: closed - Opened by bodhivani over 1 year ago - 7 comments
Labels: question

#4016 - Calculation of the non-polar part of the GBSA implicit solvents

Issue - State: closed - Opened by katzberger over 1 year ago - 2 comments
Labels: question

#4015 - Disable M1 build

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

#4014 - Add support to "NHE" C-terminal caps

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

#4013 - Improved load balancing between GPUs

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

#4002 - Increase Nonbonded threads on AMD GPUs

Pull Request - State: open - Opened by bdenhollander over 1 year ago - 9 comments

#4001 - Adding an XTC reporter

Pull Request - State: closed - Opened by RaulPPelaez over 1 year ago - 37 comments

#3995 - Restart from checkpoint or state

Issue - State: closed - Opened by SianXiaoCHN over 1 year ago - 1 comment
Labels: question

#3992 - Enable navigation between documentation versions

Issue - State: open - Opened by sef43 over 1 year ago - 13 comments
Labels: documentation

#3985 - are the latest API docs up to date?

Issue - State: closed - Opened by sef43 over 1 year ago - 5 comments

#3973 - Enable flush after enqueueReadBuffer on Windows

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

#3972 - Pressure tensor calculation every 50 timesteps

Issue - State: closed - Opened by Alexandrina-Chen over 1 year ago - 4 comments

#3963 - compile failed as generateWrappers.py has an Invalid syntax

Issue - State: closed - Opened by black6816 over 1 year ago - 3 comments

#3957 - Decomposition of energy

Issue - State: closed - Opened by UmeshRoy over 1 year ago - 11 comments

#3952 - Modify standard forces along MD

Issue - State: closed - Opened by LeonardoBarneschi over 1 year ago - 12 comments

#3949 - Setting atomic forces at each time step from python API

Issue - State: closed - Opened by dpadula85 over 1 year ago - 5 comments

#3947 - OpenCL 2.0 Shared Virtual Memory Performance

Issue - State: closed - Opened by bdenhollander over 1 year ago - 17 comments

#3944 - confused on the AttributeError

Issue - State: closed - Opened by wayuer19 over 1 year ago - 1 comment

#3943 - GLIBCXX error when attempting to import

Issue - State: open - Opened by leeping over 1 year ago - 11 comments

#3939 - Guided MD

Issue - State: open - Opened by 1heman over 1 year ago - 4 comments
Labels: question

#3937 - Investigate slow OpenCL performance on AMD

Issue - State: open - Opened by peastman over 1 year ago - 102 comments
Labels: discussion

#3929 - Porting functionality from LAMMPS for inorganic materials

Issue - State: open - Opened by philipturner over 1 year ago - 11 comments

#3927 - Multiple GPU integration problem with Openmm

Issue - State: closed - Opened by rijuaxt over 1 year ago - 4 comments
Labels: question

#3926 - PDBReporter writes incorrect box vectors if they change after loadState

Issue - State: closed - Opened by vdeshchenya over 1 year ago - 1 comment

#3924 - Optimizing findBlocksWithInteractions for M1

Issue - State: closed - Opened by philipturner over 1 year ago - 22 comments

#3922 - Saving parameters into xml is not using correct lj14scale.

Issue - State: closed - Opened by asgharrazavi over 1 year ago - 1 comment

#3908 - Confusion in improper torsion of the CustomTorsionForce.

Issue - State: closed - Opened by wayuer19 over 1 year ago - 3 comments

#3902 - Optimized reducing energy

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

#3901 - Support another GROMACS bond type

Issue - State: closed - Opened by wong105 over 1 year ago - 42 comments
Labels: enhancement

#3895 - How to make molecules rigid?

Issue - State: closed - Opened by aizvorski over 1 year ago - 2 comments
Labels: question

#3894 - Tolerance value for minimization

Issue - State: closed - Opened by jnoske over 1 year ago - 3 comments
Labels: question

#3893 - Confusion about the unit of CMAPTorsionForce in force field file

Issue - State: closed - Opened by Dead-fisher over 1 year ago - 1 comment

#3889 - FP64 emulation for Metal plugin

Issue - State: open - Opened by philipturner over 1 year ago - 49 comments

#3883 - Cuda compiler error

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

#3880 - OpenMM constant velocity steered MD

Issue - State: closed - Opened by Byun-jinyoung almost 2 years ago - 1 comment

#3869 - Protein outside the water box

Issue - State: closed - Opened by jsruizc almost 2 years ago - 1 comment

#3841 - Jumping protein

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

#3822 - Issues of simulation speed in membrane bound system

Issue - State: closed - Opened by rubinanoor9 almost 2 years ago - 3 comments

#3821 - Circular variance term for nonbonded interactions

Issue - State: closed - Opened by ZiZ1 almost 2 years ago - 2 comments

#3797 - Allow all MC barostats to scale constrainted atom groups

Pull Request - State: open - Opened by z-gong almost 2 years ago - 13 comments

#3796 - Changes to support PyPI packages

Issue - State: open - Opened by peastman almost 2 years ago - 36 comments

#3776 - How to implement a flat-bottom RMSD restraining force?

Issue - State: closed - Opened by apayne97 about 2 years ago - 20 comments

#3730 - User guide example for Small-molecule Protein Simulation broken

Issue - State: open - Opened by mganahl about 2 years ago - 6 comments

#3708 - clarification on implicit solvent parameters

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