Group Seminar Page The Forschungsseminar is a regular (weekly) meeting of the Artificial Intelligence for the Sciences Group (former Computational Molecular Biolo...
Welcome to the Artificial Intelligence for the Sciences Lectures Wiki Winter Term 20/21 * Please visit the official course catalog for more detailled infor...
Welcome to the Computer Tutorial in Markov Modeling (PyEMMA) WS 2019/20 News 10 Feb 2019: Schedule online. 16 Jan 2019: Workshop is fully booked. Dates 5 ...
Welcome to the Computer Tutorial in Markov Modeling (PyEMMA) WS 2018/19 News 21 Jan 2019: Workshop is fully booked. Please enquire after February 11 about la...
Welcome to Scientific Computing with Python, summer term 2018 News 07.06.2018 The compact course is cancelled due to organisational reasons. General Lecture I...
Dates Blockkurs 23 to 27 July 2018 9 15 h Takustr. 9 K46 (basement) News Depending on the number of participants the course may be moved from the computer ...
Berechtigungen die Sekretariat benötigt * ZEDAT Mitarbeiteraccount Antragsformular "Beschäftigte". Falls noch keine Personalnummer, zunächst Projektaccount....
Scholarships Fellowships Info and forms on this page: https://www.fu berlin.de/forschung/service/foerderung/dokumentensammlung/gast_stip/index.html#faq_stipendie...
VisitorInfo General If you plan to invite a guest scientist, contact the secretariat. There is an established routine that allows us with a minimal exchange of ...
Welcome to the Lecture Wiki of Reaktions Diffusions Simulationen für Signaltransduktionskaskaden, SoSe 2014 General Lecturer: Frank Noé Language: English/German...
Molecular Simulation II Summer term 2017 General Lecturer: Petra Imhof Computer Lab: Chris Wehmeyer, Petra Imhof Language: English Course ID: 20115901 20115...
Welcome to Reaction Diffusion Dynamics, summer term 2017 News General Lecturer: Chris Wehmeyer Assistant: Chris Fröhner, Moritz Hoffmann Language: English co...
Welcome to the Computer Tutorial in Markov Modeling (PyEMMA) WS 2017/18 News 1 Feb 2018: Workshop is fully booked. Please enquire after 12 February about las...
Welcome to Scientific Programming with Python, summer term 2018 News 16.3.: Course starts 9 April, registration via email only, see below General Lecture ID: ...
Welcome to the Computer Tutorial in Markov Modeling (PyEMMA) WS 2016/17 News For those who were not able to attend the workshop see here: Link to notebooks ...
Welcome to Reaction Diffusion Dynamics, summer term 2016 News 21.7.2016: The course has been moved to Takustr. 9, K048 (basement) 14.7.2016: Registration c...
Welcome to the Computer Tutorial in Markov Modeling (PyEMMA) WS 2015/16 News 20.1.2016: The Workshop is fully booked! If you are able to fill a last minute c...
News Registration:For resident students, prior registration in Campus Management is required.If you miss the registration date, please use the form "Modulnachmeld...
Welcome to Scientific Programming with Python, summer term 2016 News 21.7.: The course has been moved to Arnimallee 6, r. 030 (PC pool) 14.7.: Registration clo...
Welcome to Markov Chains and Markov Models summer term 2016 News 8.7. MCMM presentation dates times set. See below. General Lecture ID: 19216201 192162...
OpenMM Here I collect some tricks I found on the web and some that I've come up with to use advanced features of OpenMM. Using the group wide openmm installatio...
Allegro GPU node benchmarks This page is for all members to add their personal benchmarks of systems on the Allegro cluster for future reference a qualitative co...
Welcome to the Software Project Scientific Computing WS 2014/15 News Registration: Prior registration in either Campus Management OR KVV des Fachbereichs is re...
International Bachelor, Master and Doctoral Programmes in Germany Webseite Support:Content5 AG Iris Stengel, Tel.: 089 23685 538, i p #64;content5.de Deadline...
Welcome to the lecture wiki Stochastic Processes (winter term 2015/16) General Lecture: Felix Höfling Problems: Jan Hendrik Prinz, Felix Höfling Languag...
VMDTricks ((short description what this page is about)) enable live update of secondary structure assigment When selecting the Catoon or NewCartoon representati...
Welcome to the lecture wiki * Advanced Molecular Simulation* WS 2015/16 News Registration: Prior registration in Campus Management AND KVV des Fachbereichs is r...
Wilkommen beim Wiki der Vorlesung * Computerorientierte Mathematik II* SoSe 2015 News 05.08.: Die Nachbesprechung der Klausur findet am Donnerstag 13.8. in de...
Welcome to the Software Project Computational Physics and Scientific Computing WS 2015/16 News Registration: For resident students, prior registration in Campu...
Welcome to the Lecture Wiki of Reaktions Diffusions Simulationen für Signaltransduktionskaskaden, SoSe 2015 News 22.4.2015 Registration FU students please sig...
Welcome to the lecture wiki Advanced Molecular Simulation WS 2014/15 News Registration: Prior registration in either Campus Management OR KVV des Fachbereichs i...
Welcome to Markov Chains and Markov Models SoSe 2015 News 08.05.2015 Please find the notes used for the lectures in section Content below. We will try to upd...
Wilkommen beim Wiki der Vorlesung Computerorientierte Mathematik I WS 2014/2015 News 18.04.2015: Die Einsicht der Nachklausur findet am 22.04. statt (8:00 10:...
Welcome to Software Lab "Modern Methods of Theoretical Physics A" summer term 2015 News General Lecturer: Frank Noé, Christoph Wehmeyer Language: English...
Willkommen im Wiki der Numerik I SoSe 2014 News 15.10.: Studierende, die die Klausur zwar bestanden aber ihre Note verbessern möchten, können die Nachklausur e...
Welcome to the Computer Tutorial in Markov Modeling WS 2014/15 News Registration: Prior registration in either Campus Management OR KVV des Fachbereichs is req...
CompMolBio Web Preferences The following settings are web preferences of the CompMolBio web. These preferences overwrite the site level preferences in . and ...
Literature seminar Markov processes Students will review and present selected topics in the realm of inference and analysis of Markov processes. We will select a ...
TodayILearned Have you learned something you want to share. Something that made your work much easier. Something that everybody should avoid. Here you go... Bash...
19133 Forschungsprojekt:Moleküldynamik und Stochastische Simulation under construction Allgemein Dozent: Frank Noé Sprache: Deutsch SWS: 4 LP: 5 Termine Ers...
Welcome to the Lecture Wiki Methods of Molecular Simulation, SoSe 2014 under construction News General Lecture: Frank Noé, Petra Imhof, Nuria Plattner Exerc...
Welcome to the Lecture Wiki of Computational Molecular Physics, SoSe 2014 under construction News General Lecture: Petra Imhof, Frank Noé, Marcus Weber, Burkh...
LinuxModules This page shows you how to handle your shell environment via the linux module system Getting started Enable modules on cuda01/adagio: echo e "\nexp...
Literature Seminar: Simulation and Analysis of Stochastic Processes Seminar zu Numerik IVc (Stochastische Prozesse) General Information Lecturer: Bettina Keller...
Page LocalInstall This page shows how to install software in you home directory. Preparing the directory tree and installing the "stow" utility GNU Stow is a sma...
separate different molecules in PDB Just copy and paste the lines that belong to the molecule of interest. You may use the fields with the residue name or the cha...
Books The column "Where?" means just: Where can I find the book by default. Does not need to be updated when someone borrows the book for some time. Author T...
BMP Rezeptor brainstorming * Die Frage "was ist der Nutzen von 2 Rezeptortypen vs. 1 Rezeptortyp" ist biologisch interessant und kann durch eine Kombination vo...
Diplomarbeit Torsten Lüdge Theory Inverse Problems and Bayes Ansatz FRET Trajectory estimation: Window method, Optimal Random Walk (Probability to Obse...
Transition Path Theory of Protein:Ligand Binding Processes Goal Ziel: Modellierung der Bildung eines Kollisionskomplexes und des darauf folgenden Bindungvorgang...
Page UDPGlcNAc * PDB Entry 1VGV contains a structure of UDP GlcNAc Epimerase with bound UDP GalNAc (it rather looks like UDP ManNAc?!) * given the coordinat...
Martin Held Agenda 2010 TPT 3D * Nov 09: Pathway Figures * Nov 09: Isocommittor surfaces / lines * Nov 09: Committor vs. PMF, Erwartungswert der mindist...
Metastability, geometric clustering and PCA PCA Es wird häufig angenommen, dass die langsamen Ereignisse komplett in den ersten PCA Komponenten zu finden sind, d...
Open Scientific Questions, Problems and Trash.Projects I: Analysis and Modeling of Molecular Dynamics Essential Problems Reliable and Automatic Generation of a...
A microscopic approach towards protein folding via transition networks Goal Etablierung eines methodischen Rahmens zur Modellierung der Konformationsdynamik von...
Single Molecule FRET analysis and modeling DFG Proposal. Joint Project by Uli Nienhaus (Experiments), Helmut Grubmüller (Simulation Modeling) and Frank Noe (Model...
Software Framework for Time Series Analysis / Phase Profiler Overview SoftwareFramework_Mindmap.pdf: Mindmap of ideas for Software Framework Goal This project a...
Page BornRadii This pages list the necessary steps to calculate ''perfect'' GB radii for a structure given as PDB * generate a PQR file for the structure (usin...
Folding @ Home Berlin Overview Folding@Home (also known as FAH or F@H) is a distributed computing project designed to perform computationally intensive simulation...
ImplicitSolvation In constrast to explicit solvation models, implicit solvation treats the solvent as bulk medium. The solvent properties are implicitly modeled b...
Page AdaptiveMolecularDynamicsSimulation The main page about Adaptive Molecular Dynamics Simulation (AMoDS) Project Overview The omnipresent Sampling Problem i...
Page AdaptiveSamplingResults Overview of the Results of the Enhanced Sampling Technique so far Simulating the MR121 GSGSW We use one large simulation of the MR12...
Page BibTexTest These are some example references , , . Very nice. And here the math capabilities: %$ E=mc^2 $% \mathcal N(\mu, \sigma^2) \sim \frac {1}{\sigma\s...
Page BibTex BibTex is used for citing references in lyx and latex. Maintenance All references we use will be maintained in CiteULike Our group there is called:...
Page OpenProblemsClustering Open Problem: Incremental Clustering Introduction Currently, we are using k means clustering on a complete MD dataset to generate mic...
Transition Matrix Properties Transition matrices are so called stochastic matrices, which means, that all entries are real values between zero and one, meaning, ...
Page EnergyErrorEstimation We propose a new approximatiom to analytically predict errors in energy differences. The underlying probability of transitions between ...
Page ResultsAdaptiveFindNewStates Details about using the advanced sampling to find new states in the system as fast as possible. MR121 GSGSW We used the setup w...
Page SoftwareFrameworkLibs Attempt of an objective comparison COLT The Matrix Toolkits for Java (MTJ) JMulti Gretl Algorithm/Mechanism COLT MTJ JMult...
Page NetCDF How can we make use of the properties of NetCDF in our project? How to define a new trajectory class i. The steps to using your TrajectoryBuilderIF c...
Sensititivy Analysis in the Degenerate Case for Perron Eigenvalues We use a paper from N. Singhal and V. Pande as reference and start from there. We proceed in a...
Page DetailedBalance This is a discussion about the necessity of Detailed Balance in Markov Models Definition The probability of being in a state o at some time ...