50 recent changes in CompMolBio Web retrieved at 13:32 (GMT)

LinuxModules
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...
NumerikIVc
For lecture page see: Numerik IVc
SeminarStochastischeProzesse
Literature Seminar: Simulation and Analysis of Stochastic Processes Seminar zu Numerik IVc (Stochastische Prozesse) General Information Lecturer: Bettina Keller...
LocalInstall
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...
MDTricks
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...
BicycleRepairman
Page BicycleRepairman Bicycle Repairman is an automation tool for scientific simulations. Find it on github.
CMBBooks
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...
TGFReceptors
BMP Rezeptor brainstorming * Die Frage "was ist der Nutzen von 2 Rezeptortypen vs. 1 Rezeptortyp" ist biologisch interessant und kann durch eine Kombination vo...
TorstenTodo
Diplomarbeit Torsten Lüdge Theory Inverse Problems and Bayes Ansatz FRET Trajectory estimation: Window method, Optimal Random Walk (Probability to Obse...
TransitionPathTheoryHeld
Transition Path Theory of Protein:Ligand Binding Processes Goal Ziel: Modellierung der Bildung eines Kollisionskomplexes und des darauf folgenden Bindungvorgang...
UDPGlcNAc
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...
MartinTodo2010
Martin Held Agenda 2010 TPT 3D * Nov 09: Pathway Figures * Nov 09: Isocommittor surfaces / lines * Nov 09: Committor vs. PMF, Erwartungswert der mindist...
Metastability
Metastability, geometric clustering and PCA PCA Es wird häufig angenommen, dass die langsamen Ereignisse komplett in den ersten PCA Komponenten zu finden sind, d...
OpenProblems
Open Scientific Questions, Problems and Trash.Projects I: Analysis and Modeling of Molecular Dynamics Essential Problems Reliable and Automatic Generation of a...
PhDJanWigger
A microscopic approach towards protein folding via transition networks Goal Etablierung eines methodischen Rahmens zur Modellierung der Konformationsdynamik von...
SingleMoleculeFRET
Single Molecule FRET analysis and modeling DFG Proposal. Joint Project by Uli Nienhaus (Experiments), Helmut Grubmüller (Simulation Modeling) and Frank Noe (Model...
SoftwareFramework
Software Framework for Time Series Analysis / Phase Profiler Overview SoftwareFramework_Mindmap.pdf: Mindmap of ideas for Software Framework Goal This project a...
BornRadii
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...
FaHOverview
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
ImplicitSolvation In constrast to explicit solvation models, implicit solvation treats the solvent as bulk medium. The solvent properties are implicitly modeled b...
MartinFischbachTodo2010
Page MartinFischbachTodo2010 Martin Fischbach PhD Plans and Milestones (Mainly 2010) Software Platform * End 2009: Abschluss Architekturplanung Softwareplat...
AdaptiveMolecularDynamicsSimulation
Page AdaptiveMolecularDynamicsSimulation The main page about Adaptive Molecular Dynamics Simulation (AMoDS) Project Overview The omnipresent Sampling Problem i...
AdaptiveSamplingResults
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...
AktinAnalysis
Page AktinAnalysis TODO Person Task State Martin calculation of electrostatic potential map of (closed_atp_dimer, closed_atp),( closed_adp_dim...
ArashTodo
Structure Diploma Thesis Arash Introduction Theory Inverse Problems and Bayes Ansatz Markov chains, Markov property Forward Backward and Expectation Maximiza...
BibTexTest
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...
SamplingGroup
Page SamplingGroup ((short description what this page is about)) Section 1 ((content)) Section 2 ((content)) Comments
WinterSeminar2010
Winter seminar 2010 slides Slides Title Speaker Desc
SoftwareFrameworkDesign
Page SoftwareFrameworkDesign Software Frame Design General Inbion basecamphq Core Packages ToDo (Martin) Completed targets * (Done) Discard current interface...
CMBShirt
* Name * * Desired Number on the Back (max 2 digits)* Size Frank Noé 13 M Emal Alekozai 15 XL Arash Azhand 79 M Stefan Bernh...
PSeminar
Page PSeminar Future schedule TPT, Coarse grained Flow, PinWW Frank HMM SDE and HMM VAR ...
CSS
Center of Scientific Simulation Please go to new Wiki page: https://www.mi.fu berlin.de/w/CSS
BibTex
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:...
OpenProblemsClustering
Page OpenProblemsClustering Open Problem: Incremental Clustering Introduction Currently, we are using k means clustering on a complete MD dataset to generate mic...
TransitionMatrix
Transition Matrix Properties Transition matrices are so called stochastic matrices, which means, that all entries are real values between zero and one, meaning, ...
EnergyErrorEstimation
Page EnergyErrorEstimation We propose a new approximatiom to analytically predict errors in energy differences. The underlying probability of transitions between ...
ResultsAdaptiveFindNewStates
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...
HowTos
Page HowTos ((short description what this page is about)) Section 1 ((content)) Section 2 ((content)) Comments
SoftwareFrameworkLibs
Page SoftwareFrameworkLibs Attempt of an objective comparison COLT The Matrix Toolkits for Java (MTJ) JMulti Gretl Algorithm/Mechanism COLT MTJ JMult...
NetCDF
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...
ClosedADP
Page ClosedADP * stationary distribution over lag time:
ClosedATPfull
Page ClosedATPfull * cluster analysis combined trajectory with gaussians: * stationary distribution over time:
EigenvectorSensitivity
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...
ADPcomplete
Page ADPcomplete Analysis of complete ADP trajectory (open and closed combined) * fig.jpg: * stationary distribution over lag time: * Implie...
ATPcomplete
Page ATPcomplete Analysis of complete ATP trajectory (open and closed) * first 40000 steps belong to open state, rest to closed: * stationary dist...
DetailedBalance
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 ...
OpenProfilinATPfull
Page OpenProfilinATPfull * cluster analysis combined trajectory with gaussians:
OpenProfilinADPfull
Page OpenProfilinADPfull * cluster analysis combined trajectory with gaussians:
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Topic revision: r3 - 15 Nov 2006, ProjectContributor
 
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