User contributions for Admin

12 May 2022

• 14:3314:33, 12 May 2022 diff hist +68 MediaWiki:Sidebar No edit summary

11 May 2022

• 22:2722:27, 11 May 2022 diff hist 0 N File:LabCluster.pdf No edit summary current
• 22:2522:25, 11 May 2022 diff hist +8,178 N Lab:newuser Created page with " = How to use lab cluster = == Preparation == If you are new to Linux: [https://ryanstutorials.net/linuxtutorial/ https://ryanstutorials.net/linuxtutorial/]     == Lab cluster == === ''login'' === You need an account to login to lab cluster to use various software and perform calcualtions. We can no longer log in remotely using password. SSH key is required. '''''You have to come to the lab to do the below in person. If not, ask admin to do it for you..."
• 22:2522:25, 11 May 2022 diff hist −19 Lab:labinfo →Use lab cluster

10 May 2022

• 16:2216:22, 10 May 2022 diff hist −10 Ammm:Mm gff →Reviews
• 16:2116:21, 10 May 2022 diff hist +708 Ammm:Mm gff →Reviews
• 16:1416:14, 10 May 2022 diff hist +16,839 N Ammm:Rigid body MD (Steven 12/2) Created page with "= <span style="color: rgb(255, 102, 0);"><references />Introduction</span><br> = Image:Gay-Berne.png <br> Recall our primary motivations for coarse-graining: 1. Eliminate high frequency motions (if possible), AND, 2. Eliminate "uninteresting" degrees of freedom (both in translation and in rotation) <br> = <br><span style="color: rgb(255, 102, 0);">Rigid Body Equations of Motion </span> = *'''Linear Momentum:'''<br> 1. Definition Image:Linear mom..." current
• 16:1316:13, 10 May 2022 diff hist +66 Ammm:Coarse grain modeling No edit summary current
• 16:1316:13, 10 May 2022 diff hist +11,051 N Ammm:Coarse grain modeling Created page with "= Introduction = *The time and length scales accessible by all-atom molecular models are limited. *Common bead-springs coarse-grain models cannot represent anisotropy of proteins such as differentiation of <span class="texhtml">φ</span> and <span class="texhtml">ψ</span> angles. *Brownian dynamics used to study diffusion limited reactions. = A Coarse-Grain Model with Anisotropic vdW and Electrostatic Multipoles = *Energy functions has been developed for rigid bodi..."
• 16:1116:11, 10 May 2022 diff hist −1 Ammm:Comparative Analysis of RNA And Mfold No edit summary current
• 16:1116:11, 10 May 2022 diff hist +9,728 N Ammm:Comparative Analysis of RNA And Mfold Created page with "= Prediction of RNA Secondary Structure With Free-Energy Minimization = 400px 700px == Reasons for Predicting the RNA Secondary Structure == === Simpler problem === * RNA secondary structure has a regular structure. * The secondary structure can be broken up into helices(paired) & loops(unpaired). === Kinetics of RNA Folding === * Secondary structure forms very fast; transcription can be the rate-limiting step...."
• 16:1016:10, 10 May 2022 diff hist −197 Tutorials:amm →New procedure to study electrostatic fields in proteins (Chistina)11/23 current
• 16:1016:10, 10 May 2022 diff hist +44 Tutorials:amm →FEP/BAR, TI (Oscar) cancelled
• 16:0816:08, 10 May 2022 diff hist +69 Tutorials:amm →FEP/BAR, TI (Oscar) cancelled
• 16:0816:08, 10 May 2022 diff hist −62 Tutorials:amm →Free energy simulations (Johnny) 10/26
• 16:0716:07, 10 May 2022 diff hist +8 Ammm:MM/PBSA with amber: theory and application →Some error information current
• 16:0616:06, 10 May 2022 diff hist +11,969 N Ammm:MM/PBSA with amber: theory and application Created page with "= Introduction = MM-PBSA method implemented in AMBER is to calculate the binding free energy for the association of two proteins or protein-ligand interation. It represents the postprocessing method to evaluate free energies of binding or to calculate absolute or relative free energies of molecules in solution.The sets of structures are usually collected with molecular dynamics or Monte Carlo methods. The first application of this model in its present form was to study t..."
• 16:0616:06, 10 May 2022 diff hist +18,746 N Ammm:Flexible Docking with GOLD and GLIDE Created page with "= Introduction = Many biological processes involve binding of a protein to some target model: * Signaling mechanism between cells * Mechanical operation (e.g. muscle contraction) * Mediation of a catalytic event * ... Drugs can work as competitive inhibitors by binding to proteins more strongly than their natural partners. Laboratory techniques for drug discovery are very time-consuming and expensive, therefore, there is a great deal of interest in developing accurate..." current Tag: Visual edit: Switched
• 16:0316:03, 10 May 2022 diff hist +10 Non equilibrium method and AFM simulation w gromacs No edit summary current Tag: Visual edit
• 16:0216:02, 10 May 2022 diff hist +10,492 N Non equilibrium method and AFM simulation w gromacs Created page with "== Atomic Force Microscopy == Atomic Force Microscopy (AFM) encompasses a variety of techniques related to the use of an extremely small mechanical probe - the probe tip can have a radius as small as 2 nm - that interacts physically with the sample of interest. In addition, the probe tip can be modified with biomolecules of interest, such as single-stranded DNA, that will interact with other biomolecules on a surface. One measurement an AFM can make is the force require..."
• 16:0116:01, 10 May 2022 diff hist −21 Tutorials:amm →Headline text
• 16:0116:01, 10 May 2022 diff hist +6 Ammm:Adaptive umbrella sampling No edit summary current
• 16:0016:00, 10 May 2022 diff hist +6 Ammm:Adaptive umbrella sampling →The potential energy as the variable for adaptive umbrella sampling
• 15:5915:59, 10 May 2022 diff hist +6 Ammm:Adaptive umbrella sampling →Background of adaptive umbrella sampling
• 15:5915:59, 10 May 2022 diff hist +4,444 N Ammm:Adaptive umbrella sampling Created page with "= <span style="background-color: rgb(153,204,255)">Multicanonical ensemble </span><br> = 500px <ref>Ulrich H.E. Hansmann a, Yuko Okamoto, Comparative study of multicanonical and simulated annealing algorithms in the protein folding problem. Physica A 212 (1994) 415-437</ref> Image:Umbrella 22.PNG Image:Umbrella 23.PNG Image:Umbrella 24.PNG = <span style="background-color: rgb(153,204,255)">Background of adaptive umbrella sam..."
• 15:5915:59, 10 May 2022 diff hist −54 Tutorials:amm →REMD with gromacs (Fonner)
• 15:5715:57, 10 May 2022 diff hist +15,807 N Ammm:REMD jenny Created page with "To enable logging immediately on lonestar, "setenv LOG_BUFS 0". Otherwise the log may be empty when your job dies. Put in brun. == gromacs instruction == http://www.gromacs.org/WIKI-import/REMD Server: http://folding.bmc.uu.se/remd/ paper: http://www.rsc.org/ej/CP/2008/b716554d.pdf '''GROMACS Procedure''' (http://www.gromacs.org/WIKI-import/REMD) The setup of a REMD simulation is actually quite straightforward. The following describes the steps that lead to hav..." current
• 15:5715:57, 10 May 2022 diff hist +9,215 N Ammm:Umbrella sampling and WHAM Created page with "= <span style="background-color: rgb(153, 204, 255);">Reaction Coordinate </span><br> = *A reaction coordinate is an abstract one-dimensional coordinate which represents progress along a reaction pathway. **Real coordinate system: bond length, bond angle, torsion **Non geometric parameters: bond order, Hydrogen bonds, RMSD *Reaction coordinates are often plotted against free energy to demonstrate in some schematic form the potential energy profile associated to the..."
• 15:5715:57, 10 May 2022 diff hist +11,020 N Ammm:Free energy simulations Created page with "=Free Energy Calculations<ref name="chipot2007">[http://catalog.lib.utexas.edu/record=b5260291~S29 Frenkel, D.; Smit, B., ''Understanding molecular simulation: from algorithms to applications''. Academic: San Diego, Calif. London, 2002.]</ref><ref name="frenkel2002">[http://catalog.lib.utexas.edu/record=b6499358~S29 Chipot, C.; Pohorille, A., ''Free Energy Calculations - Theory and Applications in Chemistry and Biology''. Springer-Verlag: Berlin Heidelberg, 2007; Vol. 86..." current
• 15:5615:56, 10 May 2022 diff hist +16,840 N Ammm:Nonpolar solvation Created page with "= ''<span style="background-color: #ffcc00">'''Hydrophobicity ''' </span>'' = == <span style="background-color: #ccffc0">'''Hydrophobicity<ref>Chandler, D., "Insight Review: Interfaces and the driving force of hydrophobic assembly” Nature 437, 640-647 (2005).</ref> <ref>Chandler, D., "Two faces of water," Nature 417, 491 (2002). </ref>''' </span> == * The hydrophobic effect - the tendency for oil and water to segregate- is important in diverse phenomena. Oil and wat..." current
• 15:5515:55, 10 May 2022 diff hist +57 Ammm:Molecular surfaces No edit summary current
• 15:5515:55, 10 May 2022 diff hist +17,108 N Ammm:Molecular surfaces Created page with "= Introduction = Calculating molecular surfaces is important and useful for structure-based drug design, representing molecules and computing inter-molecular interactions. It is also useful for displaying certain molecular properties on the surface, using color-coded and texture maps. Examples of such properties include atomic charge, electrostatic potential, hydrophobicity, polarizability, etc. = Types of Molecular Surfaces = File:Surfaces.png == Van der Waals S..."
• 15:5415:54, 10 May 2022 diff hist +16,942 N Ammm:PB (APBS) Created page with "= <span style="background-color: rgb(153, 204, 255);">What is Poisson-Boltzmann Equation(PBE)?</span><span style="background-color: rgb(192, 192, 192);"> </span> = Electrostatics plays a fundamental role in virtually all processes involving biomolecules in solution. The Poisson–Boltzmann equation is a second order nonlinear partial differential equation. It is one of the most fundamental approaches to treat electrostatic effects in solution. Poisson-Boltzmann equatio..." current
• 15:5315:53, 10 May 2022 diff hist +18,042 N Ammm:Gb gk Created page with "= ''<span style="background-color: #ffcc00">'''Why Implicit Solvent Model? ''' </span>'' = == <span style="background-color: #ccffc0">'''Solvation effect''' </span> == * Solvent effect == <span style="background-color: #ccffc0">'''Explicit vs. Implicit Solvent models''' </span> == {| cellspacing="1" cellpadding="3" border="1" class="wikitable" |+ Table Explicit vs. Implicit Solvent Model |- ! Models ! Explicit Solvent Model ! Implicit Solvent Model |- ! Idea | Re..." current
• 15:5215:52, 10 May 2022 diff hist +7,237 N Ammm:QM/MM Created page with "= Introduction<br> = == What is QM/MM?<br> == *Hybrid method that QM (Quantum mechanics) and MM (molecular mechanics) calculation schemes *The system is divided into two regions **QM and MM regions **Regions are designed based on compromise in calculation time and accuracy == Why use QM/MM?<br> == *The system is too large to use ''ab initio'' calculations<br> *MM calculations do not give the "correct" answer *Processes involving change in electronic structure..." current
• 15:5215:52, 10 May 2022 diff hist +19 Ammm:Lig ion params No edit summary current Tag: Visual edit
• 15:5115:51, 10 May 2022 diff hist +30,874 N Ammm:Lig ion params Created page with "= Introduction = == Parameters in AMOEBA == *Water first being parameterized *ions, organic molecules, proteins and nucleic acids (under improvement) == How to get parameters == *Experiment *Ab initio QM *Other force field == Unique parameters in AMOEBA == *Multipole (up to quadrupole) *Polarizability *Damping factor [http://water.bme.utexas.edu/wiki/index.php/ABS:mm_mpole Electrostatic Parameters of AMOEBA] = Metal Ion Parameterization = == Why model m..."
• 15:5015:50, 10 May 2022 diff hist +30,786 N Ammm:Ff amber ligand parameter Created page with " = Introduction = [http://ambermd.org/antechamber/antechamber.html Antechamber Online Manual] == Antechamber in Amber == File:Amber_flowchart.png File:hivrt.jpg *Cartesian coordinates for each atom in the system. These usually come from Xray crystallography, NMR spectroscopy, or model-building. They should be in Protein Databank (PDB) or Tripos "mol2" format. The program LEaP provides a platform for carrying out many of these modeling tasks, but users may..." current
• 15:4915:49, 10 May 2022 diff hist −1 Ammm:Ff gau grom prdrug →Validation of Molecular Mechanics (MM) model current
• 15:4915:49, 10 May 2022 diff hist +19,163 N Ammm:Ff gau grom prdrug Created page with "= Introduction = == When do we need to create parameters? == *System size is too large for QM '''and''' *Molecule has not been parameterized for the force field being used '''or''' *Molecular environment or conformation is substantially different == Overview of parameterization: == === Quantum Mechanics (QM) === *Optimized (a.k.a. minimum energy) geometry search *Single point calculation to fit the electrostatic potential *Torsion energy profile to calculate..."
• 15:2515:25, 10 May 2022 diff hist +295 Misc:howtoedit No edit summary
• 15:2415:24, 10 May 2022 diff hist −295 Main Page →Getting started
• 03:3803:38, 10 May 2022 diff hist 0 Tinkermeeting:Harrinton2020 No edit summary current
• 03:3803:38, 10 May 2022 diff hist +9 Tinkermeeting:Harrinton2020 No edit summary
• 03:3703:37, 10 May 2022 diff hist +1 Tinkermeeting:Harrinton2020 No edit summary
• 03:3703:37, 10 May 2022 diff hist +3,843 N Tinkermeeting:Harrinton2020 Created page with "<span style="font-size:large;">'''Welcome to the Computational Biophysics Harrington Symposium Web Page!'''</span> ---- '''<span style="font-size:larger;">March 10th Annocuement: Due to the COVID-19 global outbreak, the symposium has been canceled. Our top priority is everyone’s heath and well-being.</span>''' '''<span style="font-size:larger;">Please contact Mike Schnieders with any questions (michael-schnieders@uiowa.edu).</span>'''   '''Meeting Dates..."
• 03:3603:36, 10 May 2022 diff hist +68 N Tinkermeeting:tinkermeeting2019 Created page with "https://wiki.lct.jussieu.fr/workshop/index.php/Charmm-Tinker_meeting" current
• 03:3503:35, 10 May 2022 diff hist +18 TinkerMeeting"tinkerconf No edit summary
• 03:3403:34, 10 May 2022 diff hist +296 N TinkerMeeting"tinkerconf Created page with "*TINKER Meetings **TinkerMeeting:tinkermeeting-2017| March 2017, Washington Univ. St. Louis **TinkerMeeting:tinkermeeting-2018| 2018, UT Austin **Tinkermeeting:tinkermeeting2019| 2019, Paris, joint CHARMM/Tinker meeting **Tinkermeeting:Harrinton2020| 2020 Harrington Symposium, UT Austin"
• 03:3403:34, 10 May 2022 diff hist −247 MediaWiki:Sidebar No edit summary