Search results

reservoir sampling restoration

Status: Open.

#262 In proteneer/timemachine;

· proteneer opened on Sep 1, 2020

· Updated on Sep 1, 2020

sanity check BCC coverage

Status: Open.

#353 In proteneer/timemachine;

· proteneer opened on Feb 22, 2021

· Updated on Feb 22, 2021

Protein Forcefield

Status: Open.

#281 In proteneer/timemachine;

· proteneer opened on Oct 16, 2020

· Updated on Mar 2, 2021



Allow lambda scheduling to be more flexible.

Status: Open.

#402 In proteneer/timemachine;

· proteneer opened on Apr 26, 2021

· Updated on Apr 26, 2021

2 comments

k_centroid restraint needs a guard like the harmonic bonds

Status: Open.

#417 In proteneer/timemachine;

· proteneer opened on May 6, 2021

· Updated on May 6, 2021

Create System Object

Status: Open.

#464 In proteneer/timemachine;

· proteneer opened on Jul 8, 2021

· Updated on Jul 8, 2021

Implement ability to run Potentials over subset of System

enhancementNew feature or requestNew feature or request

performanceSpeed of simulation issueSpeed of simulation issue

Status: Open.

#472 In proteneer/timemachine;

· badisa opened on Jul 20, 2021

· Updated on Jul 20, 2021

1 comment



Make reference, test argument ordering consistent in test assertions

code style

Status: Open.

#635 In proteneer/timemachine;

· mcwitt opened on Feb 15, 2022

· Updated on Feb 15, 2022

Gradient estimator precision

Status: Open.

#667 In proteneer/timemachine;

· maxentile opened on Mar 14, 2022

· Updated on Mar 14, 2022

Clean and DRY nonbonded potential code

code style

spring cleaning

Status: Open.

#639 In proteneer/timemachine;

· mcwitt opened on Feb 16, 2022

· Updated on Mar 16, 2022

Move reusable data and utilities into testsystems

Status: Open.

#710 In proteneer/timemachine;

· mcwitt opened on Apr 8, 2022

· Updated on Apr 8, 2022

Revisit conformer generation for ELF10 charges

Status: Open.

#723 In proteneer/timemachine;

· jkausrelay opened on Apr 14, 2022

· Updated on Apr 14, 2022

deboggle: Combine common return arguments into a container

spring cleaning

Status: Open.

#757 In proteneer/timemachine;

· jkausrelay opened on Jun 17, 2022

· Updated on Jun 17, 2022

Enable MCS to be more relaxed

Status: Open.

#774 In proteneer/timemachine;

· proteneer opened on Jul 22, 2022

· Updated on Jul 22, 2022

Investigate Aligning Molecules with a minimizer

cr_scipy

enhancementNew feature or requestNew feature or request

Status: Open.

#816 In proteneer/timemachine;

· badisa opened on Sep 7, 2022

· Updated on Sep 7, 2022



Possibly update charge symmetrization approach

Status: Open.

#817 In proteneer/timemachine;

· maxentile opened on Sep 7, 2022

· Updated on Sep 7, 2022

Consider updating DEFAULT_TEMP from 300 K to 298.15 K

Status: Open.

#827 In proteneer/timemachine;

· maxentile opened on Sep 13, 2022

· Updated on Sep 13, 2022

Consider stabilizing periodic_torsion for nearly collinear inputs

Status: Open.

#848 In proteneer/timemachine;

· maxentile opened on Sep 26, 2022

· Updated on Sep 26, 2022

Add tests for numerical stability of intermediates in ring closing transformations

Status: Open.

#850 In proteneer/timemachine;

· mcwitt opened on Sep 27, 2022

· Updated on Sep 27, 2022



Consider using rich

Status: Open.

#851 In proteneer/timemachine;

· maxentile opened on Sep 27, 2022

· Updated on Sep 27, 2022

Consider adding force decomposition utility

enhancementNew feature or requestNew feature or request

Status: Open.

#886 In proteneer/timemachine;

· maxentile opened on Oct 14, 2022

· Updated on Oct 14, 2022



Improve (interpretation of) per-component diagnostics?

Status: Open.

#923 In proteneer/timemachine;

· maxentile opened on Dec 5, 2022

· Updated on Dec 5, 2022

Consider unifying approach to PRNG state

Status: Open.

#980 In proteneer/timemachine;

· maxentile opened on Mar 17, 2023

· Updated on Sep 6, 2023

5 comments