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16:13, 10 May 2022 Admin talk contribs created page 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 φ and ψ 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...")
16:11, 10 May 2022 Admin talk contribs created page 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....")
16:06, 10 May 2022 Admin talk contribs created page 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...")
16:06, 10 May 2022 Admin talk contribs created page 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...") Tag: Visual edit: Switched
16:02, 10 May 2022 Admin talk contribs created page 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...")
15:59, 10 May 2022 Admin talk contribs created page Ammm:Adaptive umbrella sampling (Created page with "= Multicanonical ensemble = 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 = Background of adaptive umbrella sam...")
15:57, 10 May 2022 Admin talk contribs created page 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...")
15:57, 10 May 2022 Admin talk contribs created page Ammm:Umbrella sampling and WHAM (Created page with "= Reaction Coordinate = *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...")
15:57, 10 May 2022 Admin talk contribs created page 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...")
15:56, 10 May 2022 Admin talk contribs created page Ammm:Nonpolar solvation (Created page with "= '''''Hydrophobicity ''' '' = == '''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>''' == * The hydrophobic effect - the tendency for oil and water to segregate- is important in diverse phenomena. Oil and wat...")
15:55, 10 May 2022 Admin talk contribs created page 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...")
15:54, 10 May 2022 Admin talk contribs created page Ammm:PB (APBS) (Created page with "= What is Poisson-Boltzmann Equation(PBE)? = 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...")
15:53, 10 May 2022 Admin talk contribs created page Ammm:Gb gk (Created page with "= '''''Why Implicit Solvent Model? ''' '' = == '''Solvation effect''' == * Solvent effect == '''Explicit vs. Implicit Solvent models''' == {| cellspacing="1" cellpadding="3" border="1" class="wikitable" |+ Table Explicit vs. Implicit Solvent Model |- ! Models ! Explicit Solvent Model ! Implicit Solvent Model |- ! Idea | Re...")
15:52, 10 May 2022 Admin talk contribs created page Ammm:QM/MM (Created page with "= Introduction = == What is QM/MM? == *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? == *The system is too large to use ''ab initio'' calculations *MM calculations do not give the "correct" answer *Processes involving change in electronic structure...")
15:51, 10 May 2022 Admin talk contribs created page 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...")
15:50, 10 May 2022 Admin talk contribs created page 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...")
15:49, 10 May 2022 Admin talk contribs created page 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...")
03:37, 10 May 2022 Admin talk contribs created page Tinkermeeting:Harrinton2020 (Created page with "'''Welcome to the Computational Biophysics Harrington Symposium Web Page!''' ---- '''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.''' '''Please contact Mike Schnieders with any questions (michael-schnieders@uiowa.edu).''' '''Meeting Dates...")
03:36, 10 May 2022 Admin talk contribs created page Tinkermeeting:tinkermeeting2019 (Created page with "https://wiki.lct.jussieu.fr/workshop/index.php/Charmm-Tinker_meeting")
03:34, 10 May 2022 Admin talk contribs created page 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")
03:31, 10 May 2022 Admin talk contribs created page TinkerMeeting:tinkermeeting-2018 (Created page with "'''TINKER Modeling Workshop 2018''' == '''Dates & location''' == '''Dates: June 2-4, 2018'''(arrive on 6/1; depart 6/4 afternoon) '''Meeting room''': BME 3.204. [https://goo.gl/maps/gKHW17wcLrv Walking direction from AT&T to BME building] (15 minutes walk from AT&T to BME) '''Organizers''': Pengyu Ren (pren@mail.utexas.edu); Jay Ponder (ponder@dasher.wustl.edu); Jean-Philip Piquemal (jpp@lct.jussieu.fr) The Weather will be hot this weekend. In the morning it sho...")
03:30, 10 May 2022 Admin talk contribs created page File:Tinkerconf.png
03:30, 10 May 2022 Admin talk contribs uploaded File:Tinkerconf.png
03:23, 10 May 2022 Admin talk contribs created page TinkerMeeting:tinkermeeting-2017 (Created page with "{{DISPLAYTITLE:{{FULLPAGENAME}}}} '''[http://biomol.bme.utexas.edu/~pren/TinkerMeeting/tinker2017agenda.html Click Here for Detailed Agenda]''' The first Tinker developer’s conference was held in St. Louis in March 2017. This interdisciplinary workshop gathered theoretical chemists, biophysicists, physicists, biomedical engineers...")
03:21, 10 May 2022 Admin talk contribs created page Lab:labinfo (Created page with " = Welcome, Ren Lab Members! = == General Information == === Lab Website === [https://biomol.bme.utexas.edu/ https://biomol.bme.utexas.edu/] === Office Number === BME 3.516 === Dr. Ren's Office Number === BME 5.202M == Communication and File Sharing == === Slack === *utren.slack.com *accounts will be created for new lab members/rotation students *noteworthy channels ** **#software for discussing various lab software + issues...")
03:15, 10 May 2022 Admin talk contribs created page Tinkergpu:get rot rest (Created page with "<pre> #!/usr/bin/env python ''' Get Tinker keywords for Boresch restraint > get_rot_rest.py sample.xyz sample.key Read any traj format and "ligand keyword" from Tinker key file Print 6 distance/angle/torsion restraints and the standard state correction ''' import numpy as np import mdtraj as md import sys import os import time import scipy.optimize from scipy.spatial import distance_matrix from scipy.cluster.hierarchy import fcluster, leaders, linkage from scipy.spa...")
03:13, 10 May 2022 Admin talk contribs created page File:PL BAR softcore.pdf
03:13, 10 May 2022 Admin talk contribs uploaded File:PL BAR softcore.pdf
03:11, 10 May 2022 Admin talk contribs created page File:Pro lig BAR softcore.pdf (BAR book chapter)
03:11, 10 May 2022 Admin talk contribs uploaded File:Pro lig BAR softcore.pdf (BAR book chapter)
02:51, 10 May 2022 Admin talk contribs created page Software:tinkercpu (Created page with " = Tinker CPU = For Tinker CPU code, download from github: https://github.com/TinkerTools/tinker (git clone recommended) Then follow the compilation instructions:")
02:50, 10 May 2022 Admin talk contribs created page Software:tinkergpu (Created page with "==Tinker9 GPU molecular dynamics== Tinker GPU simulations should use Tinker9. As of 2021, we switched to Tinker9 for GPU simulations, which is similar/consistent to Tinker CPU in terms of usage/setup, is faster than OpenMM for AMOEBA and some fixed charged force fields, and has all our new development for AMOEBA+. The setup and key files used by Tinker CPU (on this wiki page) can be directly applied to Tinker9. Set "openmp-threads 1" in the key file (this is no longer...")
02:46, 10 May 2022 Admin talk contribs created page Software:tinkercpg (Created page with "==Tinker9 GPU molecular dynamics== Tinker GPU simulations should use Tinker9. As of 2021, we switched to Tinker9 for GPU simulations, which is similar/consistent to Tinker CPU in terms of usage/setup, is faster than OpenMM for AMOEBA and some fixed charged force fields, and has all our new development for AMOEBA+. The setup and key files used by Tinker CPU (on this wiki page) can be directly applied to Tinker9. Set "openmp-threads 1" in the key file (this is no longer...")
02:28, 10 May 2022 Admin talk contribs created page Software:tinker (Created page with "= Download & Install = == Tinker GPU (Tinker9) == As of early 2021, please use Tinker9 for GPU simulations. Installing & Using Tinker9 See Tinkergpu:Openmm-install for instructions for OpenMM. However, as of early 2021, the latest tinker from github has a broken interface for latest OpenMM (older version works). == Tinker CPU == For Tinker CPU code, downl...")
02:24, 10 May 2022 Admin talk contribs created page Tutorial:tinkertut (Created page with " = Purposes = This page provide tutorials on using AMOEBA force field via Tinker (CPU) and Tinker-OpenMM (GPU) programs. = Download & Install = == Tinker GPU (Tinker9) == As of early 2021, please use Tinker9 for GPU simulations. Installing & Using Tinker9 See Tinkergpu:Openmm-install for instructions for OpenMM. However, as of early 2021, the latest tinker fr...")
02:20, 10 May 2022 Admin talk contribs created page File:GLE.pdf (generalized langevin)
02:20, 10 May 2022 Admin talk contribs uploaded File:GLE.pdf (generalized langevin)
02:17, 10 May 2022 Admin talk contribs created page Ammm:stoch (Created page with "File:GLE.pdf")
02:15, 10 May 2022 Admin talk contribs created page Ammm: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}...")
02:14, 10 May 2022 Admin talk contribs created page Ammm:Md integrator (Created page with "==Integrator== For numerical integration techniques, the book '''Numerical Recipes in C''' is good reference. As we already know MD simulations 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")...")
02:14, 10 May 2022 Admin talk contribs created page Ammm: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...") Tag: Visual edit: Switched
02:11, 10 May 2022 Admin talk contribs created page Ammm: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> 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...") Tag: Visual edit: Switched
02:10, 10 May 2022 Admin talk contribs created page Ammm:Mm aplus (Created page with "=== SATP === === Charge flux === === Charge penetration === http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00267 === Charge transfer ===") Tag: Visual edit
01:48, 10 May 2022 Admin talk contribs created page Ammm:Mm ewald (Created page with "==Truncation of long-range interaction== For condense-phase simualtion, Periodic Boundary Conditon is used to avoid the boundary effect. 480px It is expensive to compute all pairs of interactions. Solution: cutoff? Longer cutoff is (may be) more accurate but more expensive. 480px ==Electrostatics== Electrostatic interactions die off very slowly. In crystal the interaction can be rather long-ranged. '''Cutoff is a bad idea.'...")
23:40, 9 May 2022 Admin talk contribs created page File:Cai-jcp-2006.pdf
23:40, 9 May 2022 Admin talk contribs uploaded File:Cai-jcp-2006.pdf
23:21, 9 May 2022 Admin talk contribs created page Tutorials:localframe (Created page with "== Multipole definition and symmetry == ==== Local frame definition (in kmpole.f of tinker source). Currently POLTYPE force to use the first two types. ==== *Z-then-X (M are atom types in the parameter file) M1 MZ MX q Dx Dy Dz Qxx Qxy Qyy Qxz Qyz Qzz Note the traceless requirements: Qxx+Qyy+Qzz=0 *bisector: (e.g. for O in water) M1 M2 -M2, or M1 -M2 M2, or M1 -M2 -M2 are equivalent (e.g. in...")
23:18, 9 May 2022 Admin talk contribs created page File:Smp.png
23:18, 9 May 2022 Admin talk contribs uploaded File:Smp.png
23:17, 9 May 2022 Admin talk contribs created page File:Localframe.png

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