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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
23:17, 9 May 2022 Admin talk contribs uploaded File:Localframe.png
23:16, 9 May 2022 Admin talk contribs created page File:DMA.png
23:16, 9 May 2022 Admin talk contribs uploaded File:DMA.png
23:15, 9 May 2022 Admin talk contribs created page File:Qtensor.png
23:15, 9 May 2022 Admin talk contribs uploaded File:Qtensor.png
23:14, 9 May 2022 Admin talk contribs created page File:Quadtensor.png
23:14, 9 May 2022 Admin talk contribs uploaded File:Quadtensor.png
23:12, 9 May 2022 Admin talk contribs created page File:Quadrupole.png
23:12, 9 May 2022 Admin talk contribs uploaded File:Quadrupole.png
23:09, 9 May 2022 Admin talk contribs created page File:N2multipole.png
23:09, 9 May 2022 Admin talk contribs uploaded File:N2multipole.png
23:07, 9 May 2022 Admin talk contribs created page Ammm:Mm mpole (Created page with "== Is electrostatic important? == '''All forces are electrostatic in nature.''' 399px == Buckingham, Advances in Chemical Physics, 12, 107-142 (1967) == https://doi.org/10.1002/9780470143582.ch2 There is now general agreement that the significant forces between atoms and molecules have an electric origin. It is true that other sources exist, such as magnetic and gravitational interactions, but these can normally be neglected. When the molecule...")

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