Molecular Modeling with Schrödinger-Suite Workshop @ LRZ


Tuesday, December 5 - Thursday, December 7, 2017


LRZ Building, Garching/Munich, Boltzmannstr. 1


The LRZ Staff together with Schrödinger software experts will conduct a "Molecular Modelling and the Schrödinger software suite" workshop 2017 at the LRZ from Dec. 5 to Dec.7. The workshop will cover fundamental principles and concepts of molecular modeling with an emphasis on molecular dynamics. We will introduce the software packages VMD, NAMD and CPMD and how to use them on HPC systems and the Remote Visualisation Server of the LRZ. The workshop addresses people with a basic understanding of molecular simulations. (e.g. nano-scientists, biologists, physicists or researchers from life-science). The third day is devoted to the Schrödinger software suite, providing a diverse set of tools for modeling and computing the structure and properties of chemical systems, antibodies and proteins. It includes applications for e.g. quantum mechanics, homology modeling, and docking. The integrated high-performance graphical interface 'Maestro' is used for preparing, running, and analyzing the computational results of the various applications.
For more details see:

Draft Agenda:

Tuesday 05thLRZ Staff : Dr. Momme Allalen, Dr. habil Gerald Mathias and Dr. Rubén García Hernández

10:00 - 12:00             Introduction to MD and QM/MM methods 
12:00 - 13:00             Lunch Break
13:00 - 17:00             Hands-on Session Interactive Molecular Modelling (IMD) with VMD, NAMD Simulation

Wednesday 06th:  LRZ Staff : Dr. Momme Allalen, Dr. habil Gerald Mathias and Dr. Rubén García Hernández

10:00 - 12:00             Hands-on Session NAMD and CPMD.
12:00 - 13:00             Lunch Break
13:00 - 17:00             NOMAD and VR Tools, LRZ CAVE, HTC VIve and Google Cardboard (Users will be shown how to prepare their own datasets for VR)

Thursday  07th: Schrodinger: Senior Application Scientist Tatjana Braun 

10:00 - 12:00 Hands-on Workshop: "Structure-Based Drug Design with Schrödinger Tools" including the Maestro 11 Interface, Protein and Ligand Preparation, and Docking with Glide

12:00 - 13:00 Lunch Break

13:00 - 15:00  Hands-on Workshop (Cont'd)

15:00 - 16:00   Seminar/Demo: Recent Software Developments and Schrödinger Advanced Tools (FEP+)

16:00 - 17:00 Discussion / Q&A

The workshop will include both lecture and hands-on training.

Contents are subject to modifications.

Gained Skills: 

After this workshop, participants ... 

  • ... will have a detailed understanding of the essential MD simulations

  • ... will have gained knowledge about Molecular Visualization 

  • ... will be able to do interactive Molecular Modelling (IMD) with VMD 

  • ...




Momme Allalen (LRZ), Gerald Mathias (LRZ), Schrodinger Developers (Schrodinger)


Via the LRZ registration form. Please choose course HMMS1W17.