Commits · e23dc9272ab4eafd72f91aace1320a7f1177ba7b · tsoc / openmm

25 Dec, 2020 1 commit
- Fixed errors passing Numpy int64 values for int arguments (#2961) · e23dc927
  peastman authored Dec 24, 2020
  
  e23dc927
20 Dec, 2020 1 commit

fix Charmm NBThole calculation bug and Improper dihedral parameter match issue (#2952) · 698769b9

qiuzy authored Dec 21, 2020

* nbthole

* Update charmmpsffile.py

* Update charmmpsffile.py

* Update charmmparameterset.py

fix multiple dihedral with the same periodicity and add a warning reminder for improper dihedral

* add test example for NBTHole

add system files of CYT-GUA-CYT DNA segment for testing NBThole

* Update TestCharmmFiles.py

698769b9

24 Nov, 2020 1 commit
- Fixed bug in addMembrane() (#2932) · 7b4927cf
  peastman authored Nov 23, 2020
  
  7b4927cf
19 Oct, 2020 1 commit
- Fix errors on Python 3.9 (#2888) · 418855e6
  peastman authored Oct 19, 2020
```
* Fix errors on Python 3.9

* Revert changes to travis builds
```
  418855e6
24 Sep, 2020 1 commit
- Fixed warnings about string comparisons (#2859) · 6ca68730
  peastman authored Sep 24, 2020
  
  6ca68730
23 Sep, 2020 1 commit
- Fixed incorrect step calculation in metadynamics (#2855) · 96ef252c
  peastman authored Sep 23, 2020
  
  96ef252c
16 Sep, 2020 1 commit
- Fixed error in parsing PSF files (#2844) · 54cc89e5
  peastman authored Sep 16, 2020
  
  54cc89e5
18 Aug, 2020 1 commit

Updated to latest values for physical constants (#2802) · b4543a46

peastman authored Aug 18, 2020

* Updated to latest values for physical constants

* Updated documentation on physical constants

* Updated Python unit definitions

* Fixed constants in test case

* Added a comment

b4543a46

08 Aug, 2020 1 commit
- Fixed typo in forcefield.py: 2DFunction -> 3DFunction · 240a1fa7
  Dann239 authored Aug 09, 2020
  
  240a1fa7
28 Jul, 2020 1 commit
- States can save integrator parameters · 694c3930
  peastman authored Jul 28, 2020
  
  694c3930
16 Jul, 2020 1 commit
- Fixed errors · c2a049b0
  Peter Eastman authored Jul 16, 2020
  
  c2a049b0
01 Jul, 2020 2 commits
- Updated Python API for AmoebaVdwForce · fddfeecb
  Peter Eastman authored Jul 01, 2020
  
  fddfeecb
- Handle overloaded functions in C and Fortran wrappers · 9f57dbb0
  Peter Eastman authored Jul 01, 2020
  
  9f57dbb0
26 Jun, 2020 2 commits
- Bug fix · 691aa78c
  Charlles Abreu authored Jun 25, 2020
  
  691aa78c
- Fixed TestMetadynamics · 697ab72e
  Charlles Abreu authored Jun 25, 2020
  
  697ab72e
25 Jun, 2020 1 commit
- Safer periodic attribute reading in ForceField · 4fa7e25d
  Charlles Abreu authored Jun 25, 2020
  
  4fa7e25d
24 Jun, 2020 2 commits
- Metadynamic with periodic 2D/3D tabulated functions · 77b488b8
  Charlles Abreu authored Jun 24, 2020
  
  77b488b8
- ForceField prepared for specification of continuous tabulated functions · 1f6f23ce
  Charlles Abreu authored Jun 24, 2020
  
  1f6f23ce
15 Jun, 2020 1 commit
- Fixed errors in test case · 756b1d91
  peastman authored Jun 15, 2020
  
  756b1d91
11 Jun, 2020 1 commit
- Added 2019 CHARMM polarizable force field · 5c83e423
  peastman authored Jun 11, 2020
  
  5c83e423
04 Jun, 2020 3 commits
- Fixed test case · 68eb50bd
  peastman authored Jun 04, 2020
  
  68eb50bd
- Default extra particle identifier is the same for reading and writing · ff4c490e
  peastman authored Jun 04, 2020
  
  ff4c490e
- Don't mark Drude particles as deuterium · 30cac992
  peastman authored Jun 04, 2020
  
  30cac992
03 Jun, 2020 1 commit
- Fixed an error using virtual sites with patches · 23ff308e
  peastman authored Jun 03, 2020
  
  23ff308e
28 May, 2020 2 commits
- Made some tests more robust · 44325d07
  peastman authored May 28, 2020
  
  44325d07
- Use integration force groups for reporters · 20185acc
  peastman authored May 28, 2020
  
  20185acc
27 May, 2020 3 commits
- A few more changes related to setIntegrationForceGroups() · 6776f49e
  peastman authored May 27, 2020
  
  6776f49e
- Checking out unnecessarily changed files from master · bff7086a
  Charlles Abreu authored May 27, 2020
  
  bff7086a
- Better data encapsulation · 8a41f6df
  Charlles Abreu authored May 27, 2020
  
  8a41f6df
22 May, 2020 1 commit
- Created MTSLangevinIntegrator · 2abfbb43
  peastman authored May 22, 2020
  
  2abfbb43
06 May, 2020 1 commit
- C++ exceptions get translated to Python OpenMMException class (#2672) · 26532ffa
  peastman authored May 06, 2020
  
  26532ffa
04 May, 2020 1 commit

Nosé Hoover Middle scheme (#2600) · 5f374e1d

Andy Simmonett authored May 04, 2020

* Convert Nose-Hoover into LF middle scheme by copying NH kernels

* Rebrand VelocityVerletIntegrator as NoseHooverIntegrator

* Consolidate NH tests

* NoseHooverChainKernel begone

* Make Windows builds happy

* Add missing header for Windows build

* Fix mistake in CommonKernels header

* Add 6th Yoshida-Suzuki and make it the default

5f374e1d

19 Apr, 2020 1 commit
- Allow rounding errors in constrain distance comparison · 53de9f14
  YevChern authored Apr 19, 2020
  
  53de9f14
18 Apr, 2020 1 commit
- Make CharmmPsfFile ignore H-H water bond that is required for rigid water with... · 250e8699
  YevChern authored Apr 18, 2020
```
Make CharmmPsfFile ignore H-H water bond that is required for rigid water with original CHARMM implementation of constrains.
```
  250e8699
10 Apr, 2020 1 commit
- Improved counting of degrees of freedom · 954b7fc6
  peastman authored Apr 10, 2020
  
  954b7fc6
05 Apr, 2020 2 commits
- Bug fix in ForceField · 9026dbe7
  Charlles Abreu authored Apr 05, 2020
  
  9026dbe7
- Continuous1D functions with periodic option in ForceField · e9912aac
  Charlles Abreu authored Apr 05, 2020
  
  e9912aac
03 Apr, 2020 1 commit
- Tested changes moved from WellTemperedMetadynamics to Metadynamics · 9dd49614
  Charlles Abreu authored Apr 03, 2020
```
- temporary class WellTemperedMetadynamics deleted
```
  9dd49614
01 Apr, 2020 1 commit
- Increased default mass for Drude particles · 66b697f4
  peastman authored Mar 31, 2020
  
  66b697f4
31 Mar, 2020 1 commit
- Added drudeMass argument for setting mass of Drude particles · 2ca67c5c
  peastman authored Mar 31, 2020
  
  2ca67c5c