# Table of contents ###### tags: `ShirtsGroupTraining` ### [Preface](/XnRas-GHQGuvgAJLDOLAbA) ### [Chapter 1: Basics of molecular simulations](/UvnMEaRWTtewFxrWko8pXw) - [Section 1: Getting on board](/WIOSLGVNQ9OhDH_4HglsnQ) - [Section 2: A qiuick introduction to molecular dynamics (MD) simulations](/rrySo7NfRemZdmuA55IHPA) - [Section 3: A quick introduction to Monte Carlo (MC) simulations](/AkLWDhW4R8S66maN3TLR_w) - [Section 4: A quick introduction to GROMACS](/lnL2gHQ9TN6PQ6xofp99fA) - [Section 5: Running a vanilla MD simulation using GROMACS](/p4OzuLdsRCStRuG_7mVyuQ) - [Section 6: Data analysis of an MD simulation](/aVYzgZYIR5GCt5u_eJFyMA) - [Section 7: Vanilla simulations of protein-ligand complexes](/Y_21DyN-TWG8O2Rs6oayiw) - [Section 8: More complicated protein-ligand binding complexes](/Q2CJEx8nTxaAjYLCs7xc1w) ### [Chapter 2: Advanced sampling methods](/fLQCBMs5SW2GCsNmQv_uxA) - [Section 1: A quick introduction to PLUMED](/lShlPYNFTFCQmUkiUDUoow) - [Section 2: Introduction to metadynamics](/CV0j-xBISUqBquOqB_5Rrw) - [Section 3: More about metadynamics](/crZKqGS1QK-9PYsFOc99iQ) - [Section 4: Umbrella sampling and potential of mean force](/Bi_fFs3XQFCZkMuL7z1XAA) - [Section 5: Free energy calculation methods](/gGpxiHqhRXOJc3SD5MhzGQ) - [Section 6: Temperature Replica exchange molecular dynamics (TREMD)](/S3Qxl2PtTMKxrDM5aa0sIQ) - [Section 7: Hamiltonian Replica exchange molecular dynamics (HREMD)](/S3Qxl2PtTMKxrDM5aa0sIQ) - [Section 8: Alchemical free energy calculations](/mWLLFWw7TImDR5A4mHw8ew) - [Section 9: Expanded ensemble simulations](/OotKbJ8iTWO9cH2NkhF4TA) - [Section 10: Combinations of advanced sampling methods, Part 1](/exVd5HHmQ1GHnFDQ1Q6QHg) - [Section 11: Combinations of advanced sampling methods, Part 2](/rTY6LFLPSVyqqwHwL-fKxg) ### [Chapter 3: Special topics](/o1mlT4JRQeCvD1u1uTpNuQ) - [Section 1: A quick introduction to deep learning and neural networks](/yclQnV3OSTKeZ9qy24Nwcw) - [Section 2: Boltzmann generators](/S2iRt-j7S-mfA6q5fgAXig) - [Section 3: CV selection methods: RAVE and SGOOP](/VrdODuXSStSbev8VvO4kug) - [Section 4: Principle of component analysis (PCA) and time-lagged component analysis (tICA)](/tYXnTaiBT9a9rxfNUsarEA) - [Section 6: More about the applications of machine learning in computational molecular science](/oIKOG1llSpSYcyzpcj3Szg) - [Section 7: Introduction to Markov-state Modeling (MSM)](/IwtwsS_FRWmBGF5HsdKaQw) - [Section 8: The usage of PyEmma and MSMBuilder](/oNmCNfwvRKi6bZ8XrYf5Bg) ### [Problem sets and tutorials](/ebUy9D6dRaCtCM8vV22X8w) - [Practice 1: Data analysis of GROMACS outputs](/QRyHshr8Q7KflzyBTLrTrg) - [Practice 2: Improving data analysis codes](/mzV4xNy3R52aOnFrZ49JmQ) - [Practice 3: A Python library of computational molecular science](/5EsD9q_eT_2jLMp8V96eHA) - [Practice 4: NVT Monte Carlo Simulations of a Lennard-Jones fluid](/DF9GFax-SbCVKB2pxcIt6A) - [Practice 5: Improving the code for running Monte Carlo simulations](/eC0o2oifQtaKJX9ADeHhhA) - [Practice 6: Gaining more insights from an MD simulation through data analysis](/WmRXJSsESZekhMl8pGeYjQ)
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