openmmtools

openmmtools copied to clipboard

ppc64le support

5

Hi I was just wondering whether there is ppc64le support, or if it is planned in the future? Thanks

BenCree

Tests failing for nightly OpenMM builds

5

Tests are failing with nightly OpenMM builds: ``` ====================================================================== FAIL: ContextCache._copy_integrator_state correctly copies state. ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/share/miniconda/envs/test/lib/python3.6/site-packages/nose/case.py", line 197, in runTest self.test(*self.arg) File "/home/runner/work/openmmtools/openmmtools/openmmtools/tests/test_cache.py", line...

jchodera

Hard-code some parameters in Custom*Force terms for alchemical factory

1

From @peastman: > Rather than using global parameters for the constants, I suggest hardcoding them in the expression. That is, add softcore_alpha=0.5; softcore_a=1; softcore_b=1; softcore_c=6 to your expression. That will...

jchodera

In `openmmtools.utils`, the function `platform_supports_precision(platform, precision)` always fails since the context cannot be generated. Instead, the call in line 551 returns a NotImplementedError: The specific call in platform_supports_precision that leads...

soerenbrandt

Expanded ensemble

5

- Include the option weight_update to perform expanded ensemble simulations - minimum_visits and beta_factor are defined by the user - set histogram as the default for flatness criteria

ajsilveira

Hi, I tried to run the test code shown in ReplicaExchangeSampler documentation. ```python #!/usr/bin/env python import math from simtk import unit from openmmtools import testsystems, states, mcmc, multistate testsystem =...

isjoung

Minimization in ReplicaExchangeSampler

4

Hello, I have been using the minimize function in ReplicaExchangeSampler to minimize a set of replicas in different alchemical states like this: _lsd_move = openmmtools.mcmc.LangevinSplittingDynamicsMove(options) repex_simulation = ReplicaExchangeSampler(mcmc_moves=lsd_move) repex_simulation.minimize()_ I...

djhuggins

Is there an "intended" way to rerun a simulation at new alchemical states?

6

I'm interested in, after running a simulation, generating the energies at a number of new energy functions given the configurations I sampled. openmmtools handles running lots of new alchemical states...

mrshirts

Example for running MPI for ReplicaExchangeSampler?

4

Is there a good example for a script that parallelizes the runs generated by ReplicaExchangeSampler over cores via MPI (or other means)? Note that are systems are small enough (

mrshirts

Issue with Hydration Free Energies with OpenMM & OpenMMTools

9

Hey guys, I was recommended to post this issue here by @jchodera. I've been trying to use openmmtools' alchemy.py code to compute solvation free energies of an ethanol molecule in...

nickjbrowning