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- 15:38, 25 May 2022 diff hist −662 Main Page current
- 17:41, 17 May 2022 diff hist +124 Tinkergpu:Tinkercpu current
- 17:06, 17 May 2022 diff hist +164 Tinkergpu:Tinkercpu
- 03:02, 16 May 2022 diff hist +103 Tinkergpu:TinkerGpu →Tinker9 Run scripts: current
- 20:45, 13 May 2022 diff hist +18 Tinkergpu:Tinker-tut →binding free energy current
- 22:22, 11 May 2022 diff hist +191 Tinkergpu:Newuser →login from your laptop on and off campus current
- 22:19, 11 May 2022 diff hist 0 Tinkergpu:Newuser →login from your laptop on and off campus
- 02:44, 10 May 2022 diff hist +450 Tinkergpu:TinkerGpu →Compiling
- 02:43, 10 May 2022 diff hist −366 Tinkergpu:TinkerGpu →Example
- 02:42, 10 May 2022 diff hist +43 Tinkergpu:TinkerGpu →How to run Tinker9 using GPU (2021)
- 02:41, 10 May 2022 diff hist +4,644 Tinkergpu:Tinkercpu
- 02:41, 10 May 2022 diff hist −4,686 Tinkergpu:Tinkercpu Blanked the page Tag: Blanking
- 02:40, 10 May 2022 diff hist +1,111 Tinkergpu:Tinkercpu
- 02:39, 10 May 2022 diff hist −1,069 Tinkergpu:WSLinstall Blanked the page current Tag: Blanking
- 02:38, 10 May 2022 diff hist +2,759 Tinkergpu:Tinkercpu
- 02:38, 10 May 2022 diff hist −2,998 Poltype:Poltype →Notes about compiling tinker 8 with OpenMP current
- 02:37, 10 May 2022 diff hist +816 N Tinkergpu:Tinkercpu Created page with " == Tinker CPU == For Tinker CPU code, download from github: [https://github.com/jayponder/tinker https://github.com/TinkerTools] (git clone recommended) Then follow the compilation instructions: [https://biomol.bme.utexas.edu/tinkergpu/index.php?title=Poltype:Poltype#Notes_about_compiling_tinker_8_with_OpenMP https://biomol.bme.utexas.edu/tinkergpu/index.php?title=Poltype:Poltype#Notes_about_compiling_tinker_8_with_OpenMP] You may also compile Tinker for..."
- 02:37, 10 May 2022 diff hist −1,253 Tinkergpu:Tinker-tut →Download & Install
- 02:37, 10 May 2022 diff hist +37 MediaWiki:Sidebar current
- 02:36, 10 May 2022 diff hist −69 Tinkergpu:TinkerGpu
- 02:35, 10 May 2022 diff hist −9 MediaWiki:Sidebar
- 02:31, 10 May 2022 diff hist +4,111 Tinkergpu:TinkerGpu
- 02:31, 10 May 2022 diff hist −4,111 Tinkergpu:Tinker-tut →How to run Tinker9 using GPU (2021)
- 02:30, 10 May 2022 diff hist −7 MediaWiki:Sidebar
- 17:49, 7 May 2022 diff hist +1 ABS:Mm gff →Molecular Mechanics current
- 17:47, 7 May 2022 diff hist +1 ABS:Mm gff →Molecular Mechanics
- 17:42, 7 May 2022 diff hist +8 ABS:Mm ewald →Particle Mesh Ewald current
- 17:41, 7 May 2022 diff hist +1 ABS:Mm ewald →Particle Mesh Ewald
- 17:41, 7 May 2022 diff hist +1 ABS:Mm gff →Reviews
- 17:40, 7 May 2022 diff hist +8 ABS:Mm gff →Reviews Tag: Manual revert
- 17:39, 7 May 2022 diff hist −8 ABS:Mm gff →Reviews Tags: Manual revert Reverted
- 17:35, 7 May 2022 diff hist +1 ABS:Mm mpole →Local frame definition current
- 17:33, 7 May 2022 diff hist 0 N File:Local frame.png current
- 17:30, 7 May 2022 diff hist −6 ABS:Mm mpole →Local frame definition
- 17:23, 7 May 2022 diff hist 0 ABS:Mm gff →Reviews Tag: Reverted
- 17:18, 7 May 2022 diff hist +8 ABS:Mm gff →Reviews Tag: Reverted
- 17:18, 7 May 2022 diff hist −6 ABS:Mm gff →Reviews
- 17:17, 7 May 2022 diff hist −1 ABS:Mm gff →Reviews
- 17:04, 7 May 2022 diff hist +1 ABS:Mm gff
- 17:52, 22 April 2022 diff hist −7 Tinkergpu:Ammm current
- 17:52, 22 April 2022 diff hist +333 ABS:Md tp →Pressure control current
- 17:49, 22 April 2022 diff hist +90 ABS:Md tp →Langevin piston
- 17:46, 22 April 2022 diff hist +32 ABS:Md tp →pressure control
- 17:34, 22 April 2022 diff hist +32 ABS:Md tp →Ensemble
- 17:33, 22 April 2022 diff hist +7 ABS:Md tp →Bussi Parrilleno
- 17:33, 22 April 2022 diff hist +8 ABS:Md tp
- 17:32, 22 April 2022 diff hist +12,761 N ABS:Md tp Created page with "== Ensemble== Typical microscopic ensembles * Microcanonical: <math>\; \Omega(E,V,N) = e^{S/k} </math> ** the probability density is proportional to <math>\delta = \aleph(q,p)-E\,</math> ---------------------- * Canonical: <math>\; Z(T,V,N) = e^{- \aleph/kT} </math> ** the probability density is proportional to <math> exp\left(-\frac{\aleph}{kT}\right)</math> --------------------------- * Grand canonical: <math>\; \Xi(T,V,\mu) = \sum_{N}^{}e^{(\mu N/kT)}{Z}_{NVT}..."
- 17:31, 22 April 2022 diff hist +6,599 N ABS:Md integrator Created page with "==Integrator== For numerical integration techniques, the book '''Numerical Recipes in C''' is good reference. As we already know MD simualtions is solving Newton's law <math>\frac{dU(x)}{dx}=m*\frac{d^2x}{dt^2}</math> using finite difference methods. The exact way to solve the ordinary differential equation depends on the integrator. A good integrator should allow *large time step (However, if the timestep is too large for system, the simulation can "blow up")..." current
- 17:29, 22 April 2022 diff hist +5,103 N ABS:Md erg Created page with "==The Liouville equation== http://en.wikipedia.org/wiki/Liouville%27s_theorem_%28Hamiltonian%29#Liouville_equation Phase space distribution conserves over time as with the density of matter (mass conservation) Liousville eq describes the time evolution of phase space distribution function (hamiltonian describes individual member of the ensemble). Consider a dynamical system with canonical coordinates <math>q_i</math> and conjugate momenta <math>p_i</math>, where <mat..." current
- 17:29, 22 April 2022 diff hist +2,455 N ABS:Md ham Created page with "Derivation of equation of motion from Lagrangian and Hamilton formulation of classical mechanics.<ref name="frenkel">Frenkel and Smit, Understanding Molecular Simulations From algorithm to Applications.</ref> <span style="font-size: larger;">The Hamiltonian and Lagrangian formulations of classical mechanics yield identical results. This is not surprising as the Hamiltonian formulation was derived from the Lagrangian equations (see section A.2). Yet, the forms of the Lag..." current
