openmmtools

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Make a shallow copy of the serialized dict in utils.deserialize before popping the module name and class

4

If I do "1.5 cycles" of serialization (i.e., serialize, deserialize the resulting dict, reserialize the result of that) I would expect that the dict for the originally serialized object would...

dwhswenson

Multi-GPU Support for multistate runs

5

I am trying to locate the openmmtools functionality that corresponds to the 'DeviceIndex' property that can be passed to openmm's Simulation() to convey the available GPU devices. I am able...

mpvenkatesh

ParallelTemperingSampler from OpenMM checkpoint file

2

I tried to run the example ParallelTemperingSampler script from a previously generated OpenMM checkpoint file. Unfortunately, I end up with following error: "Exception: All sampler states must have box_vectors defined...

nope-sto

Require temperature to be set in integrators, don't rely on some default.

mikemhenry

Charmm36 nonbonded forces with Alchemy

8

Hello, I am trying to perform alchemy using the charmm36 forcefield but I've noticed that there are remaining forces when lambda is set to 0. In the LysozymeImplicit test system...

AJZein

create_alchemical_system complains about virtual sites that I haven't defined (used parmed to create system)

1

Hello, the problem is probably more my fault than an openmmtools problem, but I don't really know how to deal with it. I am using a script that uses `create_alchemical_system`...

MauriceKarrenbrock

Hi, I am working on absolute hydration free energies in molecules that contain virtual sites and I am using alchemy.py. It appears that the virtual sites are treated the same...

bieniekmateusz

Generalize how we autodetect global controllable parameters

1

Currently, the `alchemy` module uses [this code to identify controllable alchemical global parameters](https://github.com/choderalab/openmmtools/blob/321b998fc5977a1f8893e4ad5700b1b3aef6101c/openmmtools/states.py#L3691-L3720), which is restricted to a limited list that does not include many of the alchemical parameters we...

jchodera

Ensemble validation issue for temperature replica exchange

68

I am running temperature replica exchange simulations on small coarse-grained oligomer systems (containing a single chain), and have been using an ensemble validation check on the energies for thermodynamic state...

cwalker7

I encountered this error when using adapting this example script from `perses`: https://github.com/choderalab/perses/blob/master/perses/app/relative_point_mutation_setup.py ``` from simtk.openmm.app import * from simtk.openmm import * from simtk.unit import * def run(): from pkg_resources...

yuanqing-wang