Admin: Text replacement - "ABS" to "ammm"

2022-05-09T23:03:43Z

Text replacement - "ABS" to "ammm"

Admin at 22:58, 9 May 2022

2022-05-09T22:58:26Z

← Older revision		Revision as of 22:58, 9 May 2022
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	'''Advanced Molecular Modeling Methods'''		'''Advanced Molecular Modeling Methods'''

	= ''Molecular Mechanics and Force Fields (Ren)'' =

			= ''Molecular Mechanics and Force Fields (Ren, 3 lectures)'' =

	== [[ABS:Mm_gff\|Molecular Mechanics and General force fields]] ==		== [[ABS:Mm_gff\|Molecular Mechanics and General force fields]] ==

Admin at 22:53, 9 May 2022

2022-05-09T22:53:45Z

← Older revision		Revision as of 22:53, 9 May 2022
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	'''Advanced Molecular Modeling Methods'''		'''Advanced Molecular Modeling Methods'''

			= ''Molecular Mechanics and Force Fields (Ren)'' =

	= ''Molecular Mechanics and Force Fields (Ren~~, 3 lectures~~)'' =

	== [[ABS:Mm_gff\|Molecular Mechanics and General force fields]] ==		== [[ABS:Mm_gff\|Molecular Mechanics and General force fields]] ==

Admin at 05:53, 8 May 2022

2022-05-08T05:53:38Z

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Admin at 05:53, 8 May 2022

2022-05-08T05:53:15Z

← Older revision		Revision as of 05:53, 8 May 2022
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	<math> x^2 </math>		<math> x^2 </math>

Admin: Created page with " $x^2$ "

2022-05-08T05:53:06Z

Created page with " <math> x^2 </math>"

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← Older revision		Revision as of 23:03, 9 May 2022
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	= ''Molecular Mechanics and Force Fields (Ren, 3 lectures)'' =		= ''Molecular Mechanics and Force Fields (Ren, 3 lectures)'' =

	== [[~~ABS~~:Mm_gff\|Molecular Mechanics and General force fields]] ==		== [[ammm:Mm_gff\|Molecular Mechanics and General force fields]] ==

	== [[~~ABS~~:Mm_mpole\|Electrostatic:polarizable multipole]] ==		== [[ammm:Mm_mpole\|Electrostatic:polarizable multipole]] ==

	== [[~~ABS~~:Mm_ewald\|Ewald and vdw long range correction]] ==		== [[ammm:Mm_ewald\|Ewald and vdw long range correction]] ==

	== [[~~ABS~~:Mm_aplus\|AMOEBA+]] ==		== [[ammm:Mm_aplus\|AMOEBA+]] ==

	= ''MD (Ren, 4 lectures)'' =		= ''MD (Ren, 4 lectures)'' =

	== [[~~ABS~~:Md_ham\|Lagrangian and Hamiltonian]] (Ren) ==		== [[ammm:Md_ham\|Lagrangian and Hamiltonian]] (Ren) ==

	== [[~~ABS~~:Md_erg\|Liouville Equation and Ergodicity]] ==		== [[ammm:Md_erg\|Liouville Equation and Ergodicity]] ==

	== [[~~ABS~~:Md_integrator\|Integrator and constrain]] ==		== [[ammm:Md_integrator\|Integrator and constrain]] ==

	== [[~~ABS~~:Md_tp\|Temperature and Pressure control]] ==		== [[ammm:Md_tp\|Temperature and Pressure control]] ==

	== Stochastic/Langevin/Brownian/DPD dyanmics ==		== Stochastic/Langevin/Brownian/DPD dyanmics ==
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	= ''Deriving force field parameters for a new molecule/unit'' =		= ''Deriving force field parameters for a new molecule/unit'' =

	== [[~~ABS~~:Ff_gau_grom_prdrug\|Gaussian and gromacs and prodrug server (Fonner)]] ==		== [[ammm:Ff_gau_grom_prdrug\|Gaussian and gromacs and prodrug server (Fonner)]] ==

	== [[~~ABS~~:Ff_amber_ligand_parameter\|Amber and Antechamber (Chunli)]]==		== [[ammm:Ff_amber_ligand_parameter\|Amber and Antechamber (Chunli)]]==

	== [[~~ABS~~:Lig_ion_params\|Metal ion and ligand parameterizations (Oscar) 9/30]] ==		== [[ammm:Lig_ion_params\|Metal ion and ligand parameterizations (Oscar) 9/30]] ==

	= [[~~ABS~~:QM/MM\|QM/MM (Chistina)]] =		= [[ammm:QM/MM\|QM/MM (Chistina)]] =

	= ''Implicit Solvent approach'' =		= ''Implicit Solvent approach'' =

	== [[~~ABS~~:Gb_gk\|GB/GK (Jenny 10/12)]] ==		== [[ammm:Gb_gk\|GB/GK (Jenny 10/12)]] ==

	== [[~~ABS~~:PB_(APBS)\|PB (APBS)(Yue)]] ==		== [[ammm:PB_(APBS)\|PB (APBS)(Yue)]] ==

	== [[~~ABS~~:Molecular_surfaces\|Calculation of molecular surface (Maysam)]] <span style="background-color: rgb(255, 102, 0);">10/19</span> ==		== [[ammm:Molecular_surfaces\|Calculation of molecular surface (Maysam)]] <span style="background-color: rgb(255, 102, 0);">10/19</span> ==

	== [[~~ABS~~:Nonpolar_solvation\|Nonpolar Solvation and hydrophobicity (Jenny 10/21)]] ==		== [[ammm:Nonpolar_solvation\|Nonpolar Solvation and hydrophobicity (Jenny 10/21)]] ==

	= ''Sampling'' =		= ''Sampling'' =

	== [[~~ABS~~:Free_energy_simulations\|Free energy simulations]] (Johnny) <span style="background-color: rgb(255, 102, 0);">10/26</span> ==		== [[ammm:Free_energy_simulations\|Free energy simulations]] (Johnny) <span style="background-color: rgb(255, 102, 0);">10/26</span> ==

	== [[~~ABS~~:Umbrella_sampling_and_WHAM\|Umbrella sampling and WHAM]] (Yue) <span style="background-color: rgb(255, 102, 0);">10/28</span> ==		== [[ammm:Umbrella_sampling_and_WHAM\|Umbrella sampling and WHAM]] (Yue) <span style="background-color: rgb(255, 102, 0);">10/28</span> ==

	== [[~~ABS~~:REMD_jenny\|REMD with gromacs (Fonner)]] ==		== [[ammm:REMD_jenny\|REMD with gromacs (Fonner)]] ==

	== [[~~ABS~~:REMD_jenny\|REMD with gromacs (Jenny)]] ==		== [[ammm:REMD_jenny\|REMD with gromacs (Jenny)]] ==

	== Headline text ==		== Headline text ==

	== [[~~ABS~~:Adaptive_umbrella_sampling\|Multicanonical and adaptive umbrella sampling]] (Bruce) <span style="background-color: rgb(255, 102, 0);">11/4</span> ==		== [[ammm:Adaptive_umbrella_sampling\|Multicanonical and adaptive umbrella sampling]] (Bruce) <span style="background-color: rgb(255, 102, 0);">11/4</span> ==

	== [[Non_equilibrium_method_and_AFM_simulation_w_gromacs\|Non equilibrium method and AFM simulation w gromacs]] (Tim) <span style="color: rgb(255, 102, 0);">11/11(out of town on 11/9)</span> ==		== [[Non_equilibrium_method_and_AFM_simulation_w_gromacs\|Non equilibrium method and AFM simulation w gromacs]] (Tim) <span style="color: rgb(255, 102, 0);">11/11(out of town on 11/9)</span> ==
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	= ''Protein-ligand binding'' =		= ''Protein-ligand binding'' =

	== [[~~ABS~~:Flexible_Docking_with_GOLD_and_GLIDE\|Docking (Glide and gold) and flexibility (Maysam)]] <span style="background-color: rgb(255, 102, 0);">11/16</span> ==		== [[ammm:Flexible_Docking_with_GOLD_and_GLIDE\|Docking (Glide and gold) and flexibility (Maysam)]] <span style="background-color: rgb(255, 102, 0);">11/16</span> ==

	== [[~~ABS~~:MM/PBSA_with_amber:_theory_and_application\|MM/PBSA with amber: theory and application]](chunli) <span style="background-color: rgb(255, 102, 0);">11/18</span> ==		== [[ammm:MM/PBSA_with_amber:_theory_and_application\|MM/PBSA with amber: theory and application]](chunli) <span style="background-color: rgb(255, 102, 0);">11/18</span> ==

	== FEP/BAR, TI (Oscar) cancelled ==		== FEP/BAR, TI (Oscar) cancelled ==
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	= Electrostatics =		= Electrostatics =

	== [[~~ABS~~:VSE\|<span style="color: rgb(0, 0, 0);">New procedure to study electrostatic fields in proteins (Chistina)</span>]]<span style="background-color: rgb(255, 102, 0);">'''11/23'''</span> ==		== [[ammm:VSE\|<span style="color: rgb(0, 0, 0);">New procedure to study electrostatic fields in proteins (Chistina)</span>]]<span style="background-color: rgb(255, 102, 0);">'''11/23'''</span> ==

	== [[~~ABS~~:Comparative_Analysis_of_RNA_And_Mfold\|Comparative Analysis of RNA And Mfold]] (David) <span style="background-color: rgb(255, 102, 0);">11/25</span> ==		== [[ammm:Comparative_Analysis_of_RNA_And_Mfold\|Comparative Analysis of RNA And Mfold]] (David) <span style="background-color: rgb(255, 102, 0);">11/25</span> ==

	= ''Coarse-grained modeling'' =		= ''Coarse-grained modeling'' =

	== [[~~ABS~~:Coarse_grain_modeling\|Gay-Berne and coarse-grain modeling (Johnny) 11/30]] ==		== [[ammm:Coarse_grain_modeling\|Gay-Berne and coarse-grain modeling (Johnny) 11/30]] ==

	== [[~~ABS~~:Rigid_body_MD_(Steven_12/2) \| Rigidbody mechanics]] ==		== [[ammm:Rigid_body_MD_(Steven_12/2) \| Rigidbody mechanics]] ==

Biowiki:Ammm - Revision history

Admin: Text replacement - "ABS" to "ammm"

Admin at 22:58, 9 May 2022

Admin at 22:53, 9 May 2022

Admin at 05:53, 8 May 2022

Admin at 05:53, 8 May 2022

Admin: Created page with " x^2 "

Admin: Created page with " $x^2$ "