Main public logs

Combined display of all available logs of biowiki. You can narrow down the view by selecting a log type, the username (case-sensitive), or the affected page (also case-sensitive).

• 03:37, 10 May 2022 Admin talk contribs created page 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...")
• 03:36, 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:<span style="position: absolute; clip: rect(1px 1px 1px 1px); clip: rect(1px, 1px, 1px, 1px);">{{FULLPAGENAME}}</span>}} <span style="font-size:large;">'''[http://biomol.bme.utexas.edu/~pren/TinkerMeeting/tinker2017agenda.html Click Here for Detailed Agenda]'''</span> 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> <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...") 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.'...")
• 01:42, 10 May 2022 Maintenance script talk contribs created page File:2-4-6.png (== Summary == Importing file)
• 01:42, 10 May 2022 Maintenance script talk contribs uploaded File:2-4-6.png (== Summary == Importing file) Tag: Server-side upload
• 01:42, 10 May 2022 Maintenance script talk contribs created page File:Ionprot.png (== Summary == Importing file)
• 01:42, 10 May 2022 Maintenance script talk contribs uploaded File:Ionprot.png (== Summary == Importing file) Tag: Server-side upload
• 01:42, 10 May 2022 Maintenance script talk contribs created page File:D2677ed5bdcca77fbb98f3d32439b5b3.png (== Summary == Importing file)
• 01:42, 10 May 2022 Maintenance script talk contribs uploaded File:D2677ed5bdcca77fbb98f3d32439b5b3.png (== Summary == Importing file) Tag: Server-side upload
• 01:42, 10 May 2022 Maintenance script talk contribs created page File:60ns-4fs-rib-lic.png (== Summary == Importing file)
• 01:42, 10 May 2022 Maintenance script talk contribs uploaded File:60ns-4fs-rib-lic.png (== Summary == Importing file) Tag: Server-side upload
• 01:42, 10 May 2022 Maintenance script talk contribs created page File:7b8b965ad4bca0e41ab51de7b31363a1.png (== Summary == Importing file)
• 01:42, 10 May 2022 Maintenance script talk contribs uploaded File:7b8b965ad4bca0e41ab51de7b31363a1.png (== Summary == Importing file) Tag: Server-side upload
• 01:42, 10 May 2022 Maintenance script talk contribs created page File:Scanning2.png (== Summary == Importing file)
• 01:42, 10 May 2022 Maintenance script talk contribs uploaded File:Scanning2.png (== Summary == Importing file) Tag: Server-side upload
• 01:42, 10 May 2022 Maintenance script talk contribs created page File:Gromacs flowchart.png (== Summary == Importing file)
• 01:42, 10 May 2022 Maintenance script talk contribs uploaded File:Gromacs flowchart.png (== Summary == Importing file) Tag: Server-side upload
• 01:42, 10 May 2022 Maintenance script talk contribs created page File:9bdddc229d990af90f8322ed4ff46265.png (== Summary == Importing file)
• 01:42, 10 May 2022 Maintenance script talk contribs uploaded File:9bdddc229d990af90f8322ed4ff46265.png (== Summary == Importing file) Tag: Server-side upload
• 01:42, 10 May 2022 Maintenance script talk contribs created page File:Database jenny.pdf (== Summary == Importing file)
• 01:42, 10 May 2022 Maintenance script talk contribs uploaded File:Database jenny.pdf (== Summary == Importing file) Tag: Server-side upload
• 01:42, 10 May 2022 Maintenance script talk contribs created page File:Server room 2015 July.pdf (== Summary == Importing file)
• 01:42, 10 May 2022 Maintenance script talk contribs uploaded File:Server room 2015 July.pdf (== Summary == Importing file) Tag: Server-side upload
• 01:42, 10 May 2022 Maintenance script talk contribs created page File:Gkppt1.jpg (== Summary == Importing file)
• 01:42, 10 May 2022 Maintenance script talk contribs uploaded File:Gkppt1.jpg (== Summary == Importing file) Tag: Server-side upload
• 01:42, 10 May 2022 Maintenance script talk contribs created page File:Fan brownian dynamics.pdf (== Summary == Importing file)