# BioSim Modul 2026 ## Schedule Lecture and practical course: 09.03.-25.03.2026 (Start: 9:30 am) Room: Selbstlernzentrum (Raum 26.21.01.04) **Contact person for the lecture:** Prof. Strodel (b.strodel@fz-juelich.de) **Contact persons for the practical course:** Lara Scharbert (lara.scharbert@hhu.de) Bastian Bundschuh (bastian.bundschuh@hhu.de) Chao Zhang (c.zhang@hhu.de) Bayar Boldtumur (bayar.boldtumur@etu.u-paris.fr) Timetable for practical course (P=protocol, T=tutorial): | Day | Topic | Tutor | |-|-|-| |09.03. Mo| T1_Linux (+ Jubio) & P1_VMD | Basti + Chao| |10.03. Di| T2_MD_Tutorial (setup)| Lara | |11.03. Mi| T2_MD_Tutorial (analysis)| Lara | |12.03. Do| P2_Alanin_Dipeptid (setup)| Chao | |13.03. Fr| P2_Alanin_Dipeptid (analysis) | Basti | | | | |16.03. Mo| P3_implicit_REMD (setup + analysis) | Chao | |17.03. Di| P4_Docking | Lara | |18.03. Mi| P4_Docking | Lara | |19.03. Do| P5_Python_analysis | Bayar | |20.03. Fr| P6_Membraneprotein | Basti | | | | |23.03. Mo| Paper_Simulations (setup) | Basti + Chao | |24.03. Di| Paper_Simulations (analysis) | Lara + Chao | ## Useful links * [Sciebo folder](https://uni-duesseldorf.sciebo.de/s/2aigXRBq8nzDtNC) with all relevant documents * [Upload folder](https://uni-duesseldorf.sciebo.de/s/oN3ezCc42GKcaB8) for protocols * [MD Tutorial](http://www.strodel.de/index_files/lecture/html/tutorial.html) * GROMACS: [MD algorithm](https://manual.gromacs.org/documentation/current/reference-manual/algorithms/molecular-dynamics.html), [commands](https://manual.gromacs.org/documentation/2018/user-guide/cmdline.html), [file formats](https://manual.gromacs.org/documentation/current/reference-manual/file-formats.html) and [mdp options](https://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html) * PyMOL: [wiki](https://pymolwiki.org/index.php/Main_Page) * Linux: [cheat sheet](https://linuxopsys.com/wp-content/uploads/2022/06/linux-cheat-sheet-612x792-1.png) * Vim: [cheat sheet](https://external-preview.redd.it/iigrixvxp5aYN9ox7Gr1dfI_rhLRotWlLsCafjJqjEQ.png?auto=webp&s=1594ddc17408cb9186a73c2a6d1a1bf1e00769dd) * VMD: [tutorial](http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/node2.html) * [Strodel group website](https://strodelgroup.info) ## Arrival Let us know who you are and that you are here by adding yourself to the list: | Abr. | Name | Role | Jubio private key| | -| --- | ------- | --- | | LS | Lara Scharbert | PhD student / tutor | | BB | Bastian Bundschuh| PhD student / tutor | | CZ | Chao Zhang | PhD student/ tutor | | MA | Mahin Allahyari | Master student | biosim01-jubio | | NV | Nirojah Vettivel | PhD Student (FZJ) | biosim02-jubio| | HK |Hendrik Knaup | master student|biosim03-jubio | LW |Lars Weberskirch|Bachelor student |biosim04-jubio | NE | Niclas Edelkötter | Master student (FZJ) | biosim05-jubio | AK | Alexander Kreuzkamp | Master student | biosim06-jubio | | SP | Sahar Pourmohammadi | PhD student| biosim07-jubio | | QN |Quynh Anh Laura Nguyen | Bachelor student| biosim08-jubio | | AS | Alwine Schmidt | PhD student | biosim09-jubio | | LR | Laura Röhling | Master Student | biosim10-jubio | | HS | Huaze Sun | bachelor student | biosim11-jubio | | FK | Felix Kappmeyer| |biosim12-jubio| | AM | Aysha Musayeva| Bachelor Student | biosim13-jubio| ## First steps You can log into the local computer using your HHU account. Afterwards, click at the Ubuntu-Bio account (be patient here). We recommend to mute your computer as sometimes Ubuntu might raise a warning (and very noisy) sound when e.g. you are using DEL in the terminal although there is no text to delete anymore. ### Installations Please, install vim using the following command and confirm afterwards by typing J or Y: ```$ sudo apt install vim``` To run DSSP, please run the following command from the directory where DSSP is located: ```$ export DSSP=/usr/bin/dssp``` ### Computing Cluster JUBIO To log into our computing cluster JUBIO, please download your ssh key from the [sciebo folder](https://uni-duesseldorf.sciebo.de/s/2aigXRBq8nzDtNC) with your username (biosimXX) and copy it from the Downloads directory into the ssh directory using the following command: ```$ cp ~/Downloads/biosimXX-jubio ~/.ssh/.``` And change the permissions: ```$ chmod go-wrx ~/.ssh/biosimXX-jubio``` You can now log into JUBIO using tone of the he following command: ```$ ssh -i ~/.ssh/biosimXX-jubio biosimXX@jubio.ics.kfa-juelich.de ``` Please, replace XX with your account number (biosim01 to biosim20). Download a folder from JUBIO (run the command on your local computer in the correct directory!): ```$ scp -i ~/.ssh/biosimXX-jubio -r biosimXX@jubio.ics.kfa-juelich.de:/local/jubio/biosimXX/[path to your folder] .``` ### Data handling Your computer will be resetted after restart and the data will be lost. **Take care to not shut down your computer during the course!** As you can not use the USB ports, please upload all your data to your Sciebo account (if you do not have one yet → please create one using your HHU account). You can also temporarily use JUBIO for your backup. ### Protocols During the course you can work together on the exercises, but everyone should perform the simulations and write the protocol by themselves. You don’t need to finish the whole protocol during the course, you may also write the protocol and answer the questions at home. In that case, take care to have access to your data at home and keep in mind that you might not be able to use the software needed at home. Do everything required for the protocols for which you need the software provided in the course before leaving. Once you finished the protocol, upload your document as pdf [here](https://uni-duesseldorf.sciebo.de/s/oN3ezCc42GKcaB8) and name your document with the prefix of the exercise followed by your name, e.g. ```P1_vmd_Bundschuh_Basti```. ### "Paper" Simulations For this seminar, you will work in groups with 2-3 persons. The seminar serves to understand and perform simulations. The results and discussion with respect to the paper will be summarized as a presentation, which will be graded. Following points are important: * Please, read the paper, understand it and think of your approach to conduct the simulations and analyses mentioned in the paper. * Sometimes, you will use similar simulation methods and not the exact methods mentioned in the paper. * Discuss your approach with a supervisor before starting any simulation or analysis! * You don’t need to accomplish every simulation or analysis mentioned in the paper as they contain quite extensive analyses sometimes, which you can not accomplish in 2-3 days. * Think of the most sensible selection of simulations and analyses from the paper you can conduct within 2-3 days.The third day (Wednesday, 25th of March 2026) is optional! ## How to pass the BioSim course * **Protocols**: Upload by Friday, March 27 * **Points deduction** in case of delayed submission! * **No Admission to the exam** if protocols are missing or if less than 50% of the total points are obtained * **1 bonus point** for the exam if you obtained at least 80% of the total points for each protocol * **Seminar**: date between April 13-17 (25% of your grade) * All students will give a **20-30 min presentation** (in groups of 2) * You will present a publication that you worked with ("Paper"-Simulations). * **Exam**: date between April 13-17 (75% of your grade)