From 464bd8627b1e0b7fa6a7577e3f7a9e5f6e0ca3da Mon Sep 17 00:00:00 2001 From: Raimondas Galvelis Date: Tue, 12 Jan 2021 15:17:16 +0100 Subject: [PATCH 01/71] Test Vue loader --- index.html | 29 +++++++++++++++++++++++++---- my-component.vue | 19 +++++++++++++++++++ 2 files changed, 44 insertions(+), 4 deletions(-) create mode 100644 my-component.vue diff --git a/index.html b/index.html index c27eaca..a0b188d 100644 --- a/index.html +++ b/index.html @@ -1,4 +1,27 @@ ---- + + + + + + + + +
+ +
+ + + + + +

OpenMM

A high performance toolkit for molecular simulation. Use it as a library, or as an application. We include extensive language bindings for Python, C, C++, and even Fortran. The code is open source and actively maintained on Github, licensed under MIT and LGPL. Part of the Omnia suite of tools for predictive biomolecular simulation. @@ -77,4 +98,4 @@

- + --> diff --git a/my-component.vue b/my-component.vue new file mode 100644 index 0000000..30625ea --- /dev/null +++ b/my-component.vue @@ -0,0 +1,19 @@ + + + + + \ No newline at end of file From fbaffc2720f2d0ab2cf9d321e53457cc5c075c41 Mon Sep 17 00:00:00 2001 From: Raimondas Galvelis Date: Tue, 12 Jan 2021 19:48:20 +0100 Subject: [PATCH 02/71] Fist prototype --- about.html => about.vue | 20 +++++-- home.vue | 19 ++++++ index.html | 128 ++++++++++++---------------------------- my-component.vue | 19 ------ top.vue | 17 ++++++ 5 files changed, 90 insertions(+), 113 deletions(-) rename about.html => about.vue (95%) create mode 100644 home.vue delete mode 100644 my-component.vue create mode 100644 top.vue diff --git a/about.html b/about.vue similarity index 95% rename from about.html rename to about.vue index e871aa2..a825dca 100644 --- a/about.html +++ b/about.vue @@ -1,7 +1,16 @@ ---- -layout: page -title: About OpenMM ---- + \ No newline at end of file diff --git a/home.vue b/home.vue new file mode 100644 index 0000000..b8ef892 --- /dev/null +++ b/home.vue @@ -0,0 +1,19 @@ + \ No newline at end of file diff --git a/index.html b/index.html index a0b188d..fedaf63 100644 --- a/index.html +++ b/index.html @@ -1,101 +1,51 @@ - - + + + + + OpenMM - -
- +
+ + + + + Home + About + Performance + Installation + Documentation + Support + Resources + Tutorials + + + + + + + + +
- + + + - - - + \ No newline at end of file diff --git a/my-component.vue b/my-component.vue deleted file mode 100644 index 30625ea..0000000 --- a/my-component.vue +++ /dev/null @@ -1,19 +0,0 @@ - - - - - \ No newline at end of file diff --git a/top.vue b/top.vue new file mode 100644 index 0000000..8a87fa0 --- /dev/null +++ b/top.vue @@ -0,0 +1,17 @@ + \ No newline at end of file From f3b2b5b99d01a17162ab9f51884b2149fae2c0c5 Mon Sep 17 00:00:00 2001 From: Raimondas Galvelis Date: Tue, 12 Jan 2021 21:05:17 +0100 Subject: [PATCH 03/71] Fix code highligthing --- home.vue | 27 +++++++++++++++++++++++++++ index.html | 48 +++++++++++++++++++++++++----------------------- 2 files changed, 52 insertions(+), 23 deletions(-) diff --git a/home.vue b/home.vue index b8ef892..302f6e6 100644 --- a/home.vue +++ b/home.vue @@ -15,5 +15,32 @@ + + + + + Use OpenMM from Python + + + + Script builder + + + + \ No newline at end of file diff --git a/index.html b/index.html index fedaf63..a23768d 100644 --- a/index.html +++ b/index.html @@ -5,36 +5,39 @@ + OpenMM
- - - - Home - About - Performance - Installation - Documentation - Support - Resources - Tutorials - - - - - - - - + + + + Home + About + Performance + Installation + Documentation + Support + Resources + Tutorials + + + + + + + +
- - - + + + + + \ No newline at end of file diff --git a/index.html b/index.html index 70a71b8..02cd475 100644 --- a/index.html +++ b/index.html @@ -17,7 +17,7 @@ Home About News - Performance + Benchmarks Installation Documentation Support @@ -30,7 +30,7 @@ - Empty + Empty @@ -50,6 +50,7 @@ + + \ No newline at end of file From be6978a30f3163dd08d04c917523dbd27d8deb41 Mon Sep 17 00:00:00 2001 From: Raimondas Galvelis Date: Sat, 16 Jan 2021 20:09:44 +0100 Subject: [PATCH 12/71] Add .nojekyll --- .nojekyll | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 .nojekyll diff --git a/.nojekyll b/.nojekyll new file mode 100644 index 0000000..e69de29 From b951ebefa88b76254136f2d95da2a2af209ae9cd Mon Sep 17 00:00:00 2001 From: Raimondas Galvelis Date: Sat, 16 Jan 2021 20:57:18 +0100 Subject: [PATCH 13/71] Add all tutorials --- tutorial.vue | 17 +++++++++++++++++ tutorials.vue | 47 ++++++++++++++++++++++++++++++++++++++--------- 2 files changed, 55 insertions(+), 9 deletions(-) create mode 100644 tutorial.vue diff --git a/tutorial.vue b/tutorial.vue new file mode 100644 index 0000000..7f37063 --- /dev/null +++ b/tutorial.vue @@ -0,0 +1,17 @@ + + + \ No newline at end of file diff --git a/tutorials.vue b/tutorials.vue index 597b3ad..f19799c 100644 --- a/tutorials.vue +++ b/tutorials.vue @@ -1,18 +1,47 @@ \ No newline at end of file From 966bfa6aeefdcafbbd03154217187d21260d7629 Mon Sep 17 00:00:00 2001 From: Raimondas Galvelis Date: Sat, 16 Jan 2021 21:33:13 +0100 Subject: [PATCH 14/71] Improve the news tab --- index.html | 9 ++------- news.vue | 15 +++++++++++++++ 2 files changed, 17 insertions(+), 7 deletions(-) create mode 100644 news.vue diff --git a/index.html b/index.html index a5eb387..4cd0b57 100644 --- a/index.html +++ b/index.html @@ -29,7 +29,7 @@ - + Empty @@ -37,11 +37,6 @@ -
@@ -50,7 +45,6 @@ - \ No newline at end of file From 44afdb71ff08efe686c288afa73f6189b8a4c025 Mon Sep 17 00:00:00 2001 From: Raimondas Galvelis Date: Sat, 16 Jan 2021 22:37:02 +0100 Subject: [PATCH 15/71] Add a footer --- index.html | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/index.html b/index.html index 4cd0b57..a9b8cff 100644 --- a/index.html +++ b/index.html @@ -25,7 +25,7 @@ Tutorials - + @@ -37,7 +37,12 @@ - + + + + Copyright © 2017-{{ new Date().getFullYear() }}, OpenMM team + + From 85736569383a99dcdb67722a66142ed18c63f6bc Mon Sep 17 00:00:00 2001 From: Raimondas Galvelis Date: Sat, 16 Jan 2021 22:39:00 +0100 Subject: [PATCH 16/71] Fix favicon --- favicon.ico | Bin 0 -> 1150 bytes 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 favicon.ico diff --git a/favicon.ico b/favicon.ico new file mode 100644 index 0000000000000000000000000000000000000000..e8c7693b94d7e0137a6e02401ae86cc871201029 GIT binary patch literal 1150 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mode 100644 index e8c7693b94d7e0137a6e02401ae86cc871201029..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 1150 zcmbW1OKcle6o#h~>V^eTCAvZaHqb6AHkDW+N?CwdRP7GY1rlm2A+cbCDk2pHv48~y zfk3H5L=lM)ZdF1Otdg`e^x+3_YA11=*mWlH`!$Xod&YKV=6)QH(}Ki~GrEs+?)lH$ z|G#%e)Aq?TG^9!YjCSrZO*^P*+97EYlE@$~gQm&afyW2U^QGgFsYf$Vbd=-y>)j^z zt-3ewXDE68YlE28T%%<~yyY|5ARE0FWAz7|+MLG~Tw478*tdVG3}!tuLv-qS!oDHw z>ODd|i>Os&-mIYa+8j^M@nqb`r}A z`y@vG7G?cs;@4j!cl&h~^b#2Za!!jtyXu|A7qtW<*#Pd2&g#uq*@~X0X{0cX5ZMQ_ zY>T#SXP3pc$&s(%%?ViTZgXUPnpmeHX9ulfj9l^;mi;e~4!%RrDiWT2j&AyErgq@i zicP^*B&sgo39aiJ4ojUfdErsgud#CD6?$gY)4bc>#I@VB7SEt(W(arShqBE#C568M zr+;$Ue?c+qm$T|sN3%FfOEz^r4^vHeE2(%prC931d=Z}b$VL0m z|;6sC&q0)n3F4I_{pq%=H;rr?{lvN4{P`YH!9rwcJ^1r X_lpXlNJnaWU$5Z)jeYnZ_`l=d#DR%A diff --git a/index.html b/index.html index a9b8cff..6097af5 100644 --- a/index.html +++ b/index.html @@ -6,6 +6,7 @@ + OpenMM From 71c872ba9d062485d31e66120273b81a70289cd1 Mon Sep 17 00:00:00 2001 From: Raimondas Galvelis Date: Sun, 17 Jan 2021 00:52:16 +0100 Subject: [PATCH 18/71] Improve the home tab --- example.py | 15 +++++++++++ home.vue | 73 ++++++++++++++++++++++-------------------------------- 2 files changed, 44 insertions(+), 44 deletions(-) create mode 100644 example.py diff --git a/example.py b/example.py new file mode 100644 index 0000000..e8d265d --- /dev/null +++ b/example.py @@ -0,0 +1,15 @@ +from simtk.openmm.app import * +from simtk.openmm import * +from simtk.unit import * +from sys import stdout + +pdb = PDBFile('input.pdb') +forcefield = ForceField('amber99sb.xml', 'tip3p.xml') +system = forcefield.createSystem(pdb.topology, nonbondedMethod=PME, nonbondedCutoff=1*nanometer, constraints=HBonds) +integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picoseconds) +simulation = Simulation(pdb.topology, system, integrator) +simulation.context.setPositions(pdb.positions) +simulation.minimizeEnergy() +simulation.reporters.append(PDBReporter('output.pdb', 1000)) +simulation.reporters.append(StateDataReporter(stdout, 1000, step=True, potentialEnergy=True, temperature=True)) +simulation.step(10000) \ No newline at end of file diff --git a/home.vue b/home.vue index fa3fb54..9260dda 100644 --- a/home.vue +++ b/home.vue @@ -1,46 +1,31 @@ \ No newline at end of file + + + \ No newline at end of file From 7d9a9dc9a09d0f211a132a758949b500d8d62260 Mon Sep 17 00:00:00 2001 From: Raimondas Galvelis Date: Sun, 17 Jan 2021 04:40:48 +0100 Subject: [PATCH 19/71] Improve the benchmark tab --- benchmarks.json | 12 +++++++++ benchmarks.vue | 71 ++++++++++++++++++++----------------------------- news.vue | 2 +- 3 files changed, 42 insertions(+), 43 deletions(-) create mode 100644 benchmarks.json diff --git a/benchmarks.json b/benchmarks.json new file mode 100644 index 0000000..bb1a09c --- /dev/null +++ b/benchmarks.json @@ -0,0 +1,12 @@ +{ +"speed": + [ + ["Simulation type" , "CUDA (Titan X Pascal)", "CUDA (Titan V)", "CPU (Core i7-7740X)"], + ["Implicit, 2 fs" , 927, 1004, 9.4], + ["Implicit, 5 fs HMR" , 1528, 1437, 23.2], + ["Explicit-RF, 2 fs" , 626, 697, 20.2], + ["Explicit-RF, 5 fs HMR" , 1118, 1071, 45.6], + ["Explicit-PME, 2 fs" , 393, 419, 16.5], + ["Explicit-PME, 5 fs HMR", 752, 785, 37.9] + ] +} \ No newline at end of file diff --git a/benchmarks.vue b/benchmarks.vue index 3004de7..ba2e713 100644 --- a/benchmarks.vue +++ b/benchmarks.vue @@ -10,48 +10,35 @@ \ No newline at end of file diff --git a/news.vue b/news.vue index 0fc15bb..c417ab2 100644 --- a/news.vue +++ b/news.vue @@ -1,6 +1,6 @@ From dd223b2c58b07f9f6d22b2a668e3779dc4ac4f9e Mon Sep 17 00:00:00 2001 From: Raimondas Galvelis Date: Tue, 19 Jan 2021 19:20:32 +0100 Subject: [PATCH 20/71] Finish the documentation tab --- documentation.vue | 259 +++++++++++++++++++++------------------------- 1 file changed, 120 insertions(+), 139 deletions(-) diff --git a/documentation.vue b/documentation.vue index 70f7116..f7db4b4 100644 --- a/documentation.vue +++ b/documentation.vue @@ -1,143 +1,124 @@ + \ No newline at end of file From fa74f80b687b8230601887ef3e62b17fb8a77cf8 Mon Sep 17 00:00:00 2001 From: Raimondas Galvelis Date: Tue, 19 Jan 2021 23:03:32 +0100 Subject: [PATCH 21/71] Add the people tab --- about.vue | 90 ++---------------------------------------------------- index.html | 7 +++-- people.vue | 87 ++++++++++++++++++++++++++++++++++++++++++++++++++++ 3 files changed, 93 insertions(+), 91 deletions(-) create mode 100644 people.vue diff --git a/about.vue b/about.vue index a825dca..9dab7a6 100644 --- a/about.vue +++ b/about.vue @@ -16,8 +16,6 @@
-

About OpenMM

Backed by researchers and developers from Stanford University, MSKCC, UPF, and others around the world. @@ -47,64 +45,6 @@

-

Get started quickly with the Python Wrapper

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-
from simtk.openmm.app import *
-from simtk.openmm import *
-from simtk.unit import *
-from sys import stdout
-
-pdb = PDBFile('input.pdb')
-forcefield = ForceField('amber99sb.xml', 'tip3p.xml')
-system = forcefield.createSystem(pdb.topology, nonbondedMethod=PME, nonbondedCutoff=1*nanometer, constraints=HBonds)
-integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picoseconds)
-simulation = Simulation(pdb.topology, system, integrator)
-simulation.context.setPositions(pdb.positions)
-simulation.minimizeEnergy()
-simulation.reporters.append(PDBReporter('output.pdb', 1000))
-simulation.reporters.append(StateDataReporter(stdout, 1000, step=True, potentialEnergy=True, temperature=True))
-simulation.step(10000)
-
- -
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Part of the Omnia Suite

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The cornerstone for the Omnia suite of tools for predictive biomolecular simulation. Learn more
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Current Team

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Markland Lab

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Chodera Lab

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de Fabritiis Lab

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NIH

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Current Citation

@@ -113,34 +53,8 @@ simulation.step(10000)

More publications

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OpenMM Consortium

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A community of researchers and developers supporting OpenMM.

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  • John Chodera (MSKCC)
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  • Karmen Condic-Jurkic (MSKCC)
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  • Peter Eastman (Stanford)
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  • Gianni de Fabritiis (Pompeu Fabra)
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  • Emilio Gallicchio (Brooklyn College)
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  • Jean-Philip Piquemal (Sorbonne)
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  • Jay Ponder (WashU)
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  • Josh Rackers (Sandia)
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  • Pengyu Ren (UT Austin)
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  • Julia Rice (IBM)
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  • Andy Simmonett (NIH)
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  • Bill Swope (IBM)
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Part of the Omnia Suite

+
The cornerstone for the Omnia suite of tools for predictive biomolecular simulation. Learn more

Funding

OpenMM is currently (May 2020-Apr 2021) funded by a Chan Zuckerberg Initiative Essential Open Source Software for Science grant
diff --git a/index.html b/index.html index 6097af5..c63a615 100644 --- a/index.html +++ b/index.html @@ -19,11 +19,11 @@ About News Benchmarks - Installation Documentation Support Resources Tutorials + People @@ -32,11 +32,11 @@ - Empty + @@ -67,7 +67,8 @@ 'tab-documenation': httpVueLoader('documentation.vue'), 'tab-support': httpVueLoader('support.vue'), 'tab-resources': httpVueLoader('resources.vue'), - 'tab-tutorials': httpVueLoader('tutorials.vue') + 'tab-tutorials': httpVueLoader('tutorials.vue'), + 'tab-people': httpVueLoader('people.vue') }, data: { tab: 0 } }); diff --git a/people.vue b/people.vue new file mode 100644 index 0000000..c0616bf --- /dev/null +++ b/people.vue @@ -0,0 +1,87 @@ + + + \ No newline at end of file From ce3d7f3735b6aa2fa1834fe1da47209155a357d1 Mon Sep 17 00:00:00 2001 From: Raimondas Galvelis Date: Wed, 20 Jan 2021 21:24:35 +0100 Subject: [PATCH 22/71] Organize the old stuff into one tab --- index.html | 16 +++++-------- resources.vue | 33 --------------------------- support.vue | 28 ----------------------- about.vue => tmp.vue | 53 ++++++++++++++++++++++++++++++++++++++++++++ 4 files changed, 58 insertions(+), 72 deletions(-) delete mode 100644 resources.vue delete mode 100644 support.vue rename about.vue => tmp.vue (63%) diff --git a/index.html b/index.html index c63a615..464294d 100644 --- a/index.html +++ b/index.html @@ -16,27 +16,23 @@ Home - About News Benchmarks Documentation - Support - Resources Tutorials People - + Tmp + - - - + @@ -61,14 +57,12 @@ components: { 'top': httpVueLoader('top.vue'), 'tab-home': httpVueLoader('home.vue'), - 'tab-about': httpVueLoader('about.vue'), 'tab-news': httpVueLoader('news.vue'), 'tab-benchmarks': httpVueLoader('benchmarks.vue'), 'tab-documenation': httpVueLoader('documentation.vue'), - 'tab-support': httpVueLoader('support.vue'), - 'tab-resources': httpVueLoader('resources.vue'), 'tab-tutorials': httpVueLoader('tutorials.vue'), - 'tab-people': httpVueLoader('people.vue') + 'tab-people': httpVueLoader('people.vue'), + 'tab-tmp': httpVueLoader('tmp.vue'), }, data: { tab: 0 } }); diff --git a/resources.vue b/resources.vue deleted file mode 100644 index f1dcc3c..0000000 --- a/resources.vue +++ /dev/null @@ -1,33 +0,0 @@ - - diff --git a/support.vue b/support.vue deleted file mode 100644 index b9971da..0000000 --- a/support.vue +++ /dev/null @@ -1,28 +0,0 @@ - \ No newline at end of file diff --git a/about.vue b/tmp.vue similarity index 63% rename from about.vue rename to tmp.vue index 9dab7a6..9efe9cf 100644 --- a/about.vue +++ b/tmp.vue @@ -135,5 +135,58 @@
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Resources

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Resources that make it easier to use OpenMM.

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The OpenMM team has reviewed the links on this page, but we encourage the community to add their own.

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Tools

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Omnia An open source ecosystem built around OpenMM.

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OpenMMTools Integrators, enhanced sampling methods, test systems, and alchemical factories for OpenMM.

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OpenMM Setup A graphical application to set up and run simulations with OpenMM. Includes pull-down menus, pop-up tips, error checking, and live script building capabilities.

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PME Optimizer A script to optimize the performance of PME. It runs a series of simulations and selects the parameters that give best performance for simulating a particular system on particular hardware.

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OpenMM-MD A general purpose script (with lots of comments) that uses the OpenMM Python module to drive MD simulations. Simulation options are handled via an input file. To facilitate use of the script, the available options are always printed out for you to see, along with documentation.

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Support

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For help on submitting bug reports, requesting features, etc.

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Users

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Use the Issue Tracker to file bug reports. Please include as much information about your hardware, simulation parameters, and system as possible. It is highly recommended to included serialized XML files of your System, Integrator, and State objects.

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For general help on how to use OpenMM, check out our forum or refer to our FAQ for common errors.

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If you'd like to request a new feature to be included into the next version of OpenMM, please use the Issue Tracker. Note that we have a review process, and while we will consider all requests, we cannot guarantee that they will be implemented.

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A list of recommended hardware is available here.

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Developers

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We encourage developers to use our Github Repository's Issue Tracker. Note that the discussion is highly technical and is not suitable for most users.

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+
+
+ \ No newline at end of file From d7b140e12d773d73f553f25ea711efc62bf57726 Mon Sep 17 00:00:00 2001 From: Raimondas Galvelis Date: Wed, 20 Jan 2021 23:21:04 +0100 Subject: [PATCH 23/71] Reorganize the home tab --- home.vue | 96 ++++++++++++++++++++++++++++++++++++++++++++------------ 1 file changed, 76 insertions(+), 20 deletions(-) diff --git a/home.vue b/home.vue index 9260dda..5af850e 100644 --- a/home.vue +++ b/home.vue @@ -1,24 +1,80 @@ \ No newline at end of file diff --git a/slide.vue b/slide.vue new file mode 100644 index 0000000..cb7de68 --- /dev/null +++ b/slide.vue @@ -0,0 +1,14 @@ + + + \ No newline at end of file diff --git a/tmp.vue b/tmp.vue index 9efe9cf..6f1ad87 100644 --- a/tmp.vue +++ b/tmp.vue @@ -1,63 +1,26 @@ \ No newline at end of file From 5983e6542e6de1ef7af3995e2a140e31c903f897 Mon Sep 17 00:00:00 2001 From: Raimondas Galvelis Date: Thu, 21 Jan 2021 23:56:43 +0100 Subject: [PATCH 27/71] Add tab icons --- index.html | 35 ++++++++++++++++++++++++++--------- 1 file changed, 26 insertions(+), 9 deletions(-) diff --git a/index.html b/index.html index dc051f6..a7a5795 100644 --- a/index.html +++ b/index.html @@ -5,7 +5,7 @@ - + OpenMM @@ -16,14 +16,31 @@ - Home - News - Benchmarks - Documentation - Tutorials - People + + mdi-home-outline + Home + + + mdi-newspaper-variant-outline + News + + + mdi-gauge + Benchmarks + + mdi-book-open-page-variant-outline + Documentation + + + mdi-school-outline + Tutorials + + + mdi-account-group-outline + People + Tmp - + @@ -37,7 +54,7 @@ - + Copyright © 2017-{{ new Date().getFullYear() }}, OpenMM team From f09de2b77721c9c82131ac16d8e61ee8b2dbcc20 Mon Sep 17 00:00:00 2001 From: Raimondas Galvelis Date: Fri, 22 Jan 2021 00:01:32 +0100 Subject: [PATCH 28/71] Better mactch logo colors --- home.vue | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/home.vue b/home.vue index 0dcfcb9..b2f2f8d 100644 --- a/home.vue +++ b/home.vue @@ -84,7 +84,7 @@ module.exports = { }, methods: { changeSlideColor: function() { - const colors = ['red lighten-1', 'light-green', 'light-blue', 'amber']; + const colors = ['deep-orange', 'light-green', 'light-blue', 'amber']; let nextColor = this.slideColor; while(nextColor === this.slideColor) { nextColor = colors[Math.floor(Math.random() * colors.length)] From baafa83a4b79fdfd43710a4808ca38182df022a5 Mon Sep 17 00:00:00 2001 From: Raimondas Galvelis Date: Fri, 22 Jan 2021 00:32:24 +0100 Subject: [PATCH 29/71] Clean up the temporary tab --- tmp.vue | 245 +++++++++++++++++++++++--------------------------------- 1 file changed, 101 insertions(+), 144 deletions(-) diff --git a/tmp.vue b/tmp.vue index 6f1ad87..befbc00 100644 --- a/tmp.vue +++ b/tmp.vue @@ -1,154 +1,111 @@ \ No newline at end of file From 990de24b29d12f7056f937fe52a0d14ded53a7f4 Mon Sep 17 00:00:00 2001 From: Raimondas Galvelis Date: Sat, 23 Jan 2021 01:18:53 +0100 Subject: [PATCH 30/71] Finish the benchmark tab --- benchmarks.json | 16 ++++----- benchmarks.vue | 96 ++++++++++++++++++++++++++++++++++++++++++------- tmp.vue | 5 --- 3 files changed, 92 insertions(+), 25 deletions(-) diff --git a/benchmarks.json b/benchmarks.json index bb1a09c..f9f7df3 100644 --- a/benchmarks.json +++ b/benchmarks.json @@ -1,12 +1,12 @@ { -"speed": +"dhfr": [ - ["Simulation type" , "CUDA (Titan X Pascal)", "CUDA (Titan V)", "CPU (Core i7-7740X)"], - ["Implicit, 2 fs" , 927, 1004, 9.4], - ["Implicit, 5 fs HMR" , 1528, 1437, 23.2], - ["Explicit-RF, 2 fs" , 626, 697, 20.2], - ["Explicit-RF, 5 fs HMR" , 1118, 1071, 45.6], - ["Explicit-PME, 2 fs" , 393, 419, 16.5], - ["Explicit-PME, 5 fs HMR", 752, 785, 37.9] + ["Simulation type" , "CUDA Titan X", "CUDA Titan V", "OpenCL Titan X", "OpenCL Titan V", "OpenCL Radeon", "CPU"], + ["Implicit, 2 fs" , 927, 1004, 672, 834, 403, 9.4], + ["Implicit, 5 fs HMR" , 1528, 1437, 771, 1089, 521, 23.2], + ["Explicit-RF, 2 fs" , 626, 697, 496, 627, 295, 20.2], + ["Explicit-RF, 5 fs HMR" , 1118, 1071, 677, 893, 463, 45.6], + ["Explicit-PME, 2 fs" , 393, 419, 316, 324, 163, 16.5], + ["Explicit-PME, 5 fs HMR", 752, 785, 496, 617, 317, 37.9] ] } \ No newline at end of file diff --git a/benchmarks.vue b/benchmarks.vue index ba2e713..d317322 100644 --- a/benchmarks.vue +++ b/benchmarks.vue @@ -1,27 +1,99 @@ - + - - + + + + - - - + + + + From 9c12657d5fac4f27d9116f70c072e40ab8831ea6 Mon Sep 17 00:00:00 2001 From: Raimondas Galvelis Date: Tue, 13 Apr 2021 17:59:46 +0200 Subject: [PATCH 53/71] Slowdown the carousel transition to 5 s --- home.vue | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/home.vue b/home.vue index 2f4f22b..276be31 100644 --- a/home.vue +++ b/home.vue @@ -2,7 +2,7 @@
- + Want a custom force between two atoms? No problem. Write your force expressions in string format, and OpenMM will generate blazing fast code to do just that. No more hand-writing GPU kernels. From df2166dafd4e223a9eb82b327aca8e174169342f Mon Sep 17 00:00:00 2001 From: Raimondas Galvelis Date: Tue, 13 Apr 2021 18:10:47 +0200 Subject: [PATCH 54/71] Make the expansion panels boxed in the benchmark tab --- benchmarks.vue | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/benchmarks.vue b/benchmarks.vue index d317322..3d9dec5 100644 --- a/benchmarks.vue +++ b/benchmarks.vue @@ -12,7 +12,7 @@ Dihydrofolate Reductase (DHFR) OpenMM was benchmarked on the dihydrofolate reductase (DHFR) models taken from the Joint Amber/Charmm benchmark. This is a 159 residue protein with 2489 atoms. The version used for explicit solvent simulations included 7023 TIP3P water molecules, giving a total of 23,558 atoms. All simulations used the AMBER99SB force field and a Langevin integrator, and were run with OpenMM 7.4. - + Treatment of Solvent From 02531dc0e7661a519ac291d9e740c7726de94238 Mon Sep 17 00:00:00 2001 From: Raimondas Galvelis Date: Tue, 13 Apr 2021 18:15:05 +0200 Subject: [PATCH 55/71] Fix Script Builder button --- home.vue | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/home.vue b/home.vue index 276be31..930c1b1 100644 --- a/home.vue +++ b/home.vue @@ -57,7 +57,7 @@ - Script builder + Script builder From c17939656ffdd2a7d2bcaecf2428d0a3c95d9795 Mon Sep 17 00:00:00 2001 From: Raimondas Galvelis Date: Tue, 13 Apr 2021 18:24:32 +0200 Subject: [PATCH 56/71] Expand the installation instructions --- home.vue | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/home.vue b/home.vue index 930c1b1..4960c2c 100644 --- a/home.vue +++ b/home.vue @@ -39,8 +39,11 @@ - OpenMM can be easily installed Conda package manager. Packages are available for Linux, MacOS, and Windows. - + OpenMM can be easily installed with Conda package manager. + Packages are available for Linux, MacOS, and Windows. + A command for a quick installation: + + More details are available in the documentaion. From f4cfe2232d1f5ba50cb97fab7a96ef6555c9e35d Mon Sep 17 00:00:00 2001 From: Raimondas Galvelis Date: Tue, 13 Apr 2021 18:41:33 +0200 Subject: [PATCH 57/71] Add GitHub ribbon --- index.html | 2 ++ 1 file changed, 2 insertions(+) diff --git a/index.html b/index.html index ccf1d9d..03301db 100644 --- a/index.html +++ b/index.html @@ -15,11 +15,13 @@ + OpenMM
+ From 3f40566fbedc5216394032258ddc15898c4d1c5f Mon Sep 17 00:00:00 2001 From: Raimondas Galvelis Date: Tue, 13 Apr 2021 18:52:50 +0200 Subject: [PATCH 58/71] Fix the top text --- top.vue | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/top.vue b/top.vue index 3b02fb2..e305f0f 100644 --- a/top.vue +++ b/top.vue @@ -6,7 +6,7 @@ OpenMM - A high-performance toolkit for molecular simulation. Use it as a library, or as an application. We include extensive language bindings for Python, C, C++, and even Fortran. The code is open source and actively maintained on Github, licensed under MIT and LGPL. Part of the Omnia suite of tools for predictive biomolecular simulation. + A high-performance toolkit for molecular simulation. Use it as a library, or as an application. We include extensive language bindings for Python, C, C++, and even Fortran. The code is open source and developed on GitHub, licensed under MIT and LGPL. Part of the Omnia suite of tools for predictive biomolecular simulation. From 3839aa1471f3d9fc52e7a6d775df18546a05856d Mon Sep 17 00:00:00 2001 From: Raimondas Galvelis Date: Tue, 13 Apr 2021 19:28:56 +0200 Subject: [PATCH 59/71] Fix a typo --- home.vue | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/home.vue b/home.vue index 4960c2c..0402a17 100644 --- a/home.vue +++ b/home.vue @@ -43,7 +43,7 @@ Packages are available for Linux, MacOS, and Windows. A command for a quick installation: - More details are available in the documentaion. + More details are available in the documentation. From f6d6506d932d49d851ad1045793cf8607cf3cf23 Mon Sep 17 00:00:00 2001 From: Raimondas Galvelis Date: Wed, 21 Apr 2021 19:53:09 +0200 Subject: [PATCH 60/71] Disable YouTube tracking --- documentation.vue | 6 +++--- home.vue | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/documentation.vue b/documentation.vue index 74bb558..f39fd92 100644 --- a/documentation.vue +++ b/documentation.vue @@ -47,7 +47,7 @@ OpenMM Workshop 2012
- +
@@ -55,7 +55,7 @@ OpenMM Workshop 2013
- +
@@ -63,7 +63,7 @@ OpenMM Workshop 2014
- +
diff --git a/home.vue b/home.vue index 0402a17..68e43da 100644 --- a/home.vue +++ b/home.vue @@ -27,7 +27,7 @@ - + From e3355f5ae3dfe4e48fa300887a8b220ca99b9ca8 Mon Sep 17 00:00:00 2001 From: Raimondas Galvelis Date: Wed, 21 Apr 2021 20:09:07 +0200 Subject: [PATCH 61/71] Remove a link to builder.openmm.org --- home.vue | 3 --- 1 file changed, 3 deletions(-) diff --git a/home.vue b/home.vue index 68e43da..aba2922 100644 --- a/home.vue +++ b/home.vue @@ -59,9 +59,6 @@ - - Script builder - From 540ece0eb6caf990a116372b0df89045c7f9befa Mon Sep 17 00:00:00 2001 From: Raimondas Galvelis Date: Fri, 23 Apr 2021 18:23:56 +0200 Subject: [PATCH 62/71] Change "Fork me.." to "Visit me..." --- index.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/index.html b/index.html index 03301db..68e9bee 100644 --- a/index.html +++ b/index.html @@ -21,7 +21,7 @@
- + From 7aa83e4bc9fe617e6c1ba259464fcdd304fe98d0 Mon Sep 17 00:00:00 2001 From: Raimondas Galvelis Date: Tue, 27 Apr 2021 19:03:01 +0200 Subject: [PATCH 63/71] Embbed a Google Colab notebook --- home.vue | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/home.vue b/home.vue index aba2922..e67f8a9 100644 --- a/home.vue +++ b/home.vue @@ -1,7 +1,7 @@