Ecosyste.ms: Issues

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GitHub / openmm/openmm issues and pull requests

#4179 - Coarse-grain alchemical free energy--has anyone done it in OpenMM?

Issue - State: open - Opened by JJHuse 11 months ago - 2 comments

#4178 - Loadin Allo form of amino acids

Issue - State: open - Opened by SudhanshuShanker 11 months ago - 1 comment

#4177 - Flush queue less frequently

Pull Request - State: open - Opened by peastman 11 months ago - 2 comments

#4175 - PME implementation using the CustomNonbondedForce?

Issue - State: open - Opened by zhenyuwei99 11 months ago - 5 comments

#4174 - Custom integrator for diamondoid machinery

Issue - State: open - Opened by philipturner 11 months ago - 5 comments

#4173 - One flush significantly affects AMD HIP on Windows

Issue - State: open - Opened by bdenhollander 11 months ago - 4 comments

#4172 - Unexplained crash in OpenMM_CustomIntegrator_create

Issue - State: closed - Opened by philipturner 11 months ago - 4 comments

#4171 - Simulating molecular crystals

Issue - State: open - Opened by aizvorski 11 months ago - 5 comments

#4170 - Update README.md link

Pull Request - State: closed - Opened by jempabroni 11 months ago - 1 comment

#4169 - Neighbor lists without cutoffs

Issue - State: closed - Opened by philipturner 11 months ago - 12 comments

#4168 - Fix "off by one" error in xtc time reporting.

Pull Request - State: closed - Opened by RaulPPelaez 11 months ago - 3 comments

#4167 - Create output file with append=True

Issue - State: open - Opened by davidoskky 11 months ago - 5 comments

#4166 - Building virtual site based on an arbitrary amount of atoms?

Issue - State: open - Opened by AlexanderJussupow 11 months ago - 5 comments
Labels: question

#4165 - setPositions not working

Issue - State: open - Opened by helmutcarter 11 months ago - 4 comments

#4164 - Help with addMembrane

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

#4163 - off by one error in XTCReporter time record

Issue - State: closed - Opened by sef43 11 months ago - 1 comment

#4162 - writeFile() accepts a filename instead of a file object

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

#4161 - Fix for patches that affect only bonds, not atoms

Pull Request - State: closed - Opened by peastman 11 months ago - 2 comments

#4160 - Lammps and openmm comparing

Issue - State: open - Opened by faranak1991 11 months ago - 9 comments
Labels: question

#4159 - Folding temperature from a simulated annealing

Issue - State: open - Opened by CayetanaZF 11 months ago - 2 comments
Labels: question

#4158 - Strange protein and water position in MD trajectory

Issue - State: open - Opened by GuhLelouch 11 months ago - 2 comments

#4157 - Energy minimization for protein-ligand modeling

Issue - State: open - Opened by GuhLelouch 11 months ago - 5 comments
Labels: question

#4156 - LennardJonesEnergy decomposition in openMM

Issue - State: open - Opened by smlee99 11 months ago - 1 comment

#4155 - Add in cstddef fix for pocket FFT

Pull Request - State: closed - Opened by hmacdope 11 months ago - 2 comments

#4153 - Update to a more modern version of pymbar

Pull Request - State: closed - Opened by dwilliams-nobias 11 months ago - 1 comment

#4152 - Parametrize protein with uncapped residues

Issue - State: closed - Opened by aizvorski 11 months ago - 3 comments

#4151 - Charge scaling in electrostatic interaction depending on the atom indices

Issue - State: open - Opened by praban07 11 months ago - 15 comments

#4150 - Scaled charges for a subset of atoms

Issue - State: open - Opened by praban07 11 months ago - 2 comments
Labels: question

#4148 - Fixed numeric overflow in computing interaction groups

Pull Request - State: closed - Opened by peastman 11 months ago - 1 comment

#4147 - Use large blocks to optimize building the neighbor list

Pull Request - State: closed - Opened by peastman 12 months ago - 32 comments

#4146 - Always use nvrtc for compilation

Pull Request - State: closed - Opened by peastman 12 months ago

#4144 - Fix bug in CpuNeighborList::Voxels::getVoxelIndex()

Pull Request - State: closed - Opened by lhycms 12 months ago - 1 comment

#4142 - log file/checkpoint file discord

Issue - State: open - Opened by camKD 12 months ago - 2 comments

#4141 - An issue in CpuNeighborList.cpp

Issue - State: closed - Opened by lhycms 12 months ago - 10 comments
Labels: bug

#4140 - python 3.7 CI failing

Issue - State: closed - Opened by sef43 12 months ago - 1 comment

#4139 - GBNeck2 Energy

Issue - State: open - Opened by ajtyadav 12 months ago - 1 comment
Labels: question

#4138 - Improve documentation of LangevinIntegrator

Pull Request - State: closed - Opened by plainerman 12 months ago - 3 comments

#4137 - GRADIENT -- Illegal Value for the Total Potential Energy

Issue - State: closed - Opened by heman3333 12 months ago - 2 comments

#4136 - Using LJPME on a CustomNonbondedForce

Issue - State: closed - Opened by AnastasiaCroitoru 12 months ago - 4 comments
Labels: question

#4135 - Wrong formula for Langevin Integrator (at least in the documentation)

Issue - State: closed - Opened by plainerman 12 months ago - 3 comments
Labels: question

#4134 - Continuing the metadynamics simulation

Issue - State: closed - Opened by smlee99 12 months ago - 4 comments

#4133 - Undefined reference -- OpenMM 8.0.0 installation #2075

Issue - State: closed - Opened by pietro-sillano 12 months ago - 8 comments

#4132 - Equations for calculating non-bonded energies

Issue - State: closed - Opened by asgharrazavi 12 months ago - 20 comments

#4131 - Platform parameter settings

Issue - State: closed - Opened by Drawthe 12 months ago - 2 comments

#4130 - Throw exception when specifying properties without a Platform

Pull Request - State: closed - Opened by peastman 12 months ago

#4129 - platform properties ignored unless platform specified explicitly

Issue - State: closed - Opened by lgsmith 12 months ago - 3 comments

#4128 - Fixed DOF calculation for NoseHooverIntegrator

Pull Request - State: closed - Opened by peastman 12 months ago

#4126 - Problem with SMD

Issue - State: closed - Opened by hang921727 about 1 year ago - 7 comments

#4125 - Problem with jumping molecules (again)

Issue - State: open - Opened by leeping about 1 year ago - 14 comments

#4124 - TestOpenCLDrudeNoseHooverSingle failing repeatedly on Jenkins CI

Issue - State: closed - Opened by jchodera about 1 year ago - 1 comment

#4123 - Docs CI frequently fails due to sporadic link checking issues

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

#4122 - any way to run gromacs simulation in openmm successfully

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

#4120 - Fixed edge case in Modeller._CellList

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

#4119 - another attempted fix for MonteCarloBarostat

Pull Request - State: closed - Opened by sef43 about 1 year ago - 17 comments

#4118 - Any way to get details of Energy Minimization?

Issue - State: closed - Opened by BarCollignon about 1 year ago - 6 comments

#4117 - Problem with jumping molecules

Issue - State: closed - Opened by leeping about 1 year ago - 11 comments

#4116 - Add an option to force the timestep to be a specified value in `benchark.py`

Pull Request - State: closed - Opened by hmacdope about 1 year ago - 3 comments

#4115 - Change default plugin directory?

Issue - State: closed - Opened by BarCollignon about 1 year ago - 4 comments

#4113 - modeller: Convey bond info when adding Modellers

Pull Request - State: closed - Opened by zanebeckwith about 1 year ago - 1 comment

#4112 - Modeller.add ignores bond orders and types

Issue - State: closed - Opened by zanebeckwith about 1 year ago - 2 comments
Labels: bug

#4111 - Add timestep CLI option to `benchmark.py` example

Issue - State: closed - Opened by hmacdope about 1 year ago - 1 comment

#4110 - Draft integration of the Alchemical Transfer Method (ATM) plugin

Pull Request - State: closed - Opened by egallicc about 1 year ago - 74 comments

#4109 - Degrees of freedom for Nose-Hoover

Issue - State: closed - Opened by peastman about 1 year ago - 1 comment

#4108 - Attempt at fixing CI failure

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

#4107 - Stop simulation on the fly when a value (of a CV/OP) is hit

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

#4106 - Attempt at fixing errors with barostat

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

#4105 - Stop supporting nvcc for compilation?

Issue - State: closed - Opened by peastman about 1 year ago - 6 comments

#4104 - addSolvent now only replaces newly added water molecules with ions

Pull Request - State: closed - Opened by richardjgowers about 1 year ago - 4 comments

#4103 - Exclude specific waters from ion replacement `Modeller.addSolvent`

Issue - State: closed - Opened by IAlibay about 1 year ago - 1 comment
Labels: bug

#4102 - Local resampling trick

Issue - State: open - Opened by jchodera about 1 year ago - 6 comments

#4101 - Can't follow up from equilibration.xml or .chk - Particle is NaN

Issue - State: closed - Opened by pipitoludovico about 1 year ago - 2 comments

#4100 - Nose Hoover Friction Coefficient/Debugging the Step Function

Issue - State: closed - Opened by wlai0611 about 1 year ago - 8 comments

#4099 - Per-Particle (Pair) Evaluation of a ComputedValue

Issue - State: closed - Opened by jaketanderson about 1 year ago - 2 comments

#4098 - Decreased default epsilon for AmoebaMultipoleForce

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

#4097 - segmentation fault on mamba openmm install

Issue - State: closed - Opened by dominicrufa about 1 year ago - 4 comments

#4092 - Default values for AMOEBA polarization

Issue - State: closed - Opened by piia600 about 1 year ago - 5 comments

#4083 - is it possible to report the potential energy while minimizing?

Issue - State: open - Opened by hima111997 about 1 year ago - 1 comment

#4082 - using amber generated ligand parameter files to create system in OpenMM

Issue - State: closed - Opened by 1heman about 1 year ago - 2 comments

#4081 - Allow negative pressure in MonteCarloAnisotropicBarostat

Pull Request - State: closed - Opened by sef43 about 1 year ago - 1 comment

#4080 - RPMDIntegrator is sometimes unreliable

Issue - State: open - Opened by cihe13375 about 1 year ago

#4079 - Integrators use double precision constants in mixed precision mode

Pull Request - State: open - Opened by peastman about 1 year ago

#4078 - AmberPrmTop calls computePeriodicBoxVectors using same angle for alpha, beta, and gamma

Issue - State: open - Opened by lohedges about 1 year ago - 10 comments
Labels: enhancement

#4077 - RPMDIntegrator does not integrate at double precision at mixed prec mode

Issue - State: open - Opened by cihe13375 about 1 year ago - 5 comments
Labels: bug

#4076 - MonteCarloAnisotropicBarostat doesn't allow negative pressure

Issue - State: closed - Opened by sef43 about 1 year ago - 1 comment

#4075 - Add link to cookbook and tutorials in docs

Pull Request - State: open - Opened by sef43 about 1 year ago - 2 comments

#4074 - Added eV as an energy unit

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

#4073 - openmm.OpenMMException Error

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

#4072 - Is it possible to run OpenMM on more than node using CPU?

Issue - State: open - Opened by hima111997 about 1 year ago - 6 comments

#4071 - Differences in volume ensemble sampling

Issue - State: closed - Opened by balazsfabian about 1 year ago - 27 comments

#4070 - Skip neighbor list for very small systems

Pull Request - State: closed - Opened by peastman about 1 year ago - 14 comments