Page ADPcomplete Analysis of complete ADP trajectory (open and closed combined) * fig.jpg: * stationary distribution over lag time: * Implied ...

Page ATPcomplete Analysis of complete ATP trajectory (open and closed) * first 40000 steps belong to open state, rest to closed: * stationary distribution ...

Page AdaptiveMolecularDynamicsSimulation The main page about Adaptive Molecular Dynamics Simulation (AMoDS) Project Overview The omnipresent Sampling Problem is ...

Page AdaptiveSamplingResults Overview of the Results of the Enhanced Sampling Technique so far Simulating the MR121 GSGSW We use one large simulation of the MR121 ...

Page AktinAnalysis TODO Person Task State Martin calculation of electrostatic potential map of (closed_atp_dimer, closed_atp),( closed_adp_dimer ...

Structure Diploma Thesis Arash Introduction Theory Inverse Problems and Bayes Ansatz Markov chains, Markov property Forward Backward and Expectation Maximization ...

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 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\sqrt ...

Page BicycleRepairman Bicycle Repairman is an automation tool for scientific simulations. Find it on github.

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 (using ...

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 Title ...

* Name * * Desired Number on the Back (max 2 digits)* Size Frank Noé 13 M Emal Alekozai 15 XL Arash Azhand 79 M Stefan Bernhard ...

Center of Scientific Simulation Please go to new Wiki page: https://www.mi.fu berlin.de/w/CSS

Page ClosedADP * stationary distribution over lag time:

Page ClosedADPfull

Page ClosedATP Analysis results of closed ATP trajectories * cluster analysis first trajectory: * 2nd trj: * 3rd trj: * 4th trj: ...

Page ClosedATPfull * cluster analysis combined trajectory with gaussians: * stationary distribution over time:

Cluster Collection of information regarding the cluster. Slurm / Allegro related information The official Allegro wiki can be found here. There are different nodes ...

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 10:00 ...

Wilkommen beim Wiki der Vorlesung * Computerorientierte Mathematik II* SoSe 2015 News 05.08.: Die Nachbesprechung der Klausur findet am Donnerstag 13.8. in der ...

Welcome to the Lecture Wiki of Computational Molecular Physics, SoSe 2014 under construction News General Lecture: Petra Imhof, Frank Noé, Marcus Weber, Burkhard ...

„International Bachelor, Master and Doctoral Programmes in Germany“ Webseite Support:Content5 AG Iris Stengel, Tel.: 089 23685 538, i p #64;content5.de Deadlines ...

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 should ...

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 analogy ...

Welcome to the Computer Tutorial in Markov Modeling WS 2014/15 News Registration: Prior registration in either Campus Management OR KVV des Fachbereichs is required ...

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 cancellation ...

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 the Computer Tutorial in Markov Modeling (PyEMMA) WS 2017/18 News 1 Feb 2018: Workshop is fully booked. Please enquire after 12 February about last ...

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 last ...

Page EnergyErrorEstimation We propose a new approximatiom to analytically predict errors in energy differences. The underlying probability of transitions between states ...

Folding @ Home Berlin Overview Folding@Home (also known as FAH or F@H) is a distributed computing project designed to perform computationally intensive simulations ...

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 comparisons ...

GitSCM Summary of frequently used Git commmands. Section 1 Push my branch to the remote repository. git push origin mybranch Comments

Group Seminar Page The Forschungsseminar is a regular (weekly) meeting of the Computational Molecular Biology group. Primarily a platform for theses and dissertation ...

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ImplicitSolvation In constrast to explicit solvation models, implicit solvation treats the solvent as bulk medium. The solvent properties are implicitly modeled by ...

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 number ...

Welcome to the CMB Lectures Wiki This wiki complements the more static information in the official course catalog and also includes information on summer/winter schools ...

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 "\nexport ...

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 small ...

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 chain ...

News Registration:For resident students, prior registration in Campus Management is required.If you miss the registration date, please use the form "Modulnachmeldung ...

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 update ...

Page MartinFischbachTodo2010 Martin Fischbach PhD Plans and Milestones (Mainly 2010) Software Platform * End 2009: Abschluss Architekturplanung Softwareplattform ...

Martin Held Agenda 2010 TPT 3D * Nov 09: Pathway Figures * Nov 09: Isocommittor surfaces / lines * Nov 09: Committor vs. PMF, Erwartungswert der mindist ...

Welcome to Markov Chains and Markov Models summer term 2016 News 8.7. MCMM presentation dates times set. See below. General Lecture ID: 19216201 19216202 ...

Metastability, geometric clustering and PCA PCA Es wird häufig angenommen, dass die langsamen Ereignisse komplett in den ersten PCA Komponenten zu finden sind, da ...

Welcome to the Lecture Wiki Methods of Molecular Simulation, SoSe 2014 under construction News General Lecture: Frank Noé, Petra Imhof, Nuria Plattner Exercise ...

19133 Forschungsprojekt:Moleküldynamik und Stochastische Simulation under construction Allgemein Dozent: Frank Noé Sprache: Deutsch SWS: 4 LP: 5 Termine Erster ...

Molecular Simulation II Summer term 2017 General Lecturer: Petra Imhof Computer Lab: Chris Wehmeyer, Petra Imhof Language: English Course ID: 20115901 20115902 ...

Content to follow

Welcome to the lecture wiki Advanced Molecular Simulation WS 2014/15 News Registration: Prior registration in either Campus Management OR KVV des Fachbereichs is ...

Welcome to the lecture wiki * Advanced Molecular Simulation* WS 2015/16 News Registration: Prior registration in Campus Management AND KVV des Fachbereichs is required ...

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 class ...

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 ...

For lecture page see: Numerik IVc

Berechtigungen die Sekretariat benötigt * ZEDAT Mitarbeiteraccount Antragsformular "Beschäftigte". Falls noch keine Personalnummer, zunächst Projektaccount ...

Page OpenADP Analysis results of open ADP trajectories * 1st trj: * 2nd trj: * 3rd trj: * 4th trj: * 5th trj: ...

Page OpenADPfull * cluster analysis combined trajectory with gaussians:

Page OpenATP Analysis results of open ATP trajectories * 1st trj: * 2nd trj: * 3rd trj: * 4th trj: * 5th trj: ...

Page OpenATPfull * cluster analysis combined trajectory with gaussians:

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 installation ...

Open Scientific Questions, Problems and Trash.Projects I: Analysis and Modeling of Molecular Dynamics Essential Problems Reliable and Automatic Generation of a ...

Page OpenProblemsClustering Open Problem: Incremental Clustering Introduction Currently, we are using k means clustering on a complete MD dataset to generate microstates ...

Page OpenProfilinADP Analysis results of open profilin ADP trajectories * 1st trj: * 2nd trj: * 3rd trj: * 4th trj: * 5th ...

Page OpenProfilinADPfull * cluster analysis combined trajectory with gaussians:

Page OpenProfilinATP Analysis results of open profilin ATP trajectories * 1st trj: * 2nd trj: * 3rd trj: * 4th trj: * 5th ...

Page OpenProfilinATPfull * cluster analysis combined trajectory with gaussians:

Page PSeminar Future schedule TPT, Coarse grained Flow, PinWW Frank HMM SDE and HMM VAR ...

A microscopic approach towards protein folding via transition networks Goal Etablierung eines methodischen Rahmens zur Modellierung der Konformationsdynamik von ...

Welcome to the Lecture Wiki of Reaktions Diffusions Simulationen für Signaltransduktionskaskaden, SoSe 2014 General Lecturer: Frank Noé Language: English/German ...

Welcome to the Lecture Wiki of Reaktions Diffusions Simulationen für Signaltransduktionskaskaden, SoSe 2015 News 22.4.2015 Registration FU students please sign ...

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 closed ...

Welcome to Reaction Diffusion Dynamics, summer term 2017 News General Lecturer: Chris Wehmeyer Assistant: Chris Fröhner, Moritz Hoffmann Language: English course ...

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 lab ...

* Office hardware list * HPC resources

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 with ...

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 Veranstaltungsname Semester News Allgemeines Vorlesung: Übungen: Sprache: SWS: ; LPs/Credits: Zielgruppe: Voraussetzungen ...

Welcome to the lecture/seminar wiki Veranstaltungsname Semester News General Lecture: Exercises: Language: Students: Requirements: Objectives: ...

Page SamplingGroup ((short description what this page is about)) Section 1 ((content)) Section 2 ((content)) Comments

Scholarships Fellowships Info and forms on this page: https://www.fu berlin.de/forschung/service/foerderung/dokumentensammlung/gast_stip/index.html#faq_stipendien ...

Welcome to Scientific Computing with Python, summer term 2018 News 07.06.2018 The compact course is cancelled due to organisational reasons. General Lecture ID ...

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 closed ...

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: 19226811 ...

Literature Seminar: Simulation and Analysis of Stochastic Processes Seminar zu Numerik IVc (Stochastische Prozesse) General Information Lecturer: Bettina Keller ...

Single Molecule FRET analysis and modeling DFG Proposal. Joint Project by Uli Nienhaus (Experiments), Helmut Grubmüller (Simulation Modeling) and Frank Noe (Modeling ...

Welcome to the Software Project Computational Physics and Scientific Computing WS 2015/16 News Registration: For resident students, prior registration in Campus ...

Software Framework for Time Series Analysis / Phase Profiler Overview SoftwareFramework_Mindmap.pdf: Mindmap of ideas for Software Framework Goal This project aims ...

Page SoftwareFrameworkDesign Software Frame Design General Inbion basecamphq Core Packages ToDo (Martin) Completed targets * (Done) Discard current interface ...

Page SoftwareFrameworkLibs Attempt of an objective comparison COLT The Matrix Toolkits for Java (MTJ) JMulti Gretl Algorithm/Mechanism COLT MTJ JMulti ...

Welcome to the Software Project Scientific Computing WS 2014/15 News Registration: Prior registration in either Campus Management OR KVV des Fachbereichs is required ...

Welcome to the lecture wiki Stochastic Processes (winter term 2015/16) General Lecture: Felix Höfling Problems: Jan Hendrik Prinz, Felix Höfling Language ...

BMP Rezeptor brainstorming * Die Frage "was ist der Nutzen von 2 Rezeptortypen vs. 1 Rezeptortyp" ist biologisch interessant und kann durch eine Kombination von ...

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 ...

Diplomarbeit Torsten Lüdge Theory Inverse Problems and Bayes Ansatz FRET Trajectory estimation: Window method, Optimal Random Walk (Probability to Observe ...

Transition Matrix Properties Transition matrices are so called stochastic matrices, which means, that all entries are real values between zero and one, meaning, that ...

Transition Path Theory of Protein:Ligand Binding Processes Goal Ziel: Modellierung der Bildung eines Kollisionskomplexes und des darauf folgenden Bindungvorgangs ...

Page UDPGlcNAc * PDB Entry 1VGV contains a structure of UDP GlcNAc Epimerase with bound UDP GalNAc (it rather looks like UDP ManNAc?!) * given the coordinates ...

VMDTricks ((short description what this page is about)) enable live update of secondary structure assigment When selecting the Catoon or NewCartoon representation ...

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 emails ...

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