Detailed topic list for CompMolBio Web

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

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

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

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

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\s...

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 (usin...

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...

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

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:

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:...

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

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

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 ...

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...

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...

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...

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 las...

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 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 ...

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

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

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...

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 Artificial Intelligence for the Sciences Group (former Computational Molecular Biolo...

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

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

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 ...

Welcome to the Artificial Intelligence for the Sciences Lectures Wiki Winter Term 20/21 * Please visit the official course catalog and the Wiki page for inf...

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...

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...

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 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...

Welcome to the Computer Tutorial in Markov Modeling WS 2020/21 News 23 Feb 2021: The course is booked out. 05 Feb 2021: This year's workshop will for t...

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

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 192162...

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

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