Preparing for molecular dynamics simulations

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/ please see click for Yang lab website /

Helpful links for Pharm528/BioC430

1. VMD win mac ER ERwat

2. Cygwin if you use PC (another good option is NX).

It seems the default installation does not include SSH (needed to make a connection to HPCC). You can update the installation by re-clicking the .EXE file. During the installation, search the package OPENSSH and make sure OPENSSH is clicked (instead of skipped). It should work if you finish the rest of this update process.

3. Unix primer HTML PDF


5. emacs HTML PDF


7. Get a HPCC account via faculty Account

8. AMBER (more to come)

9. How to perform a simple MD simulation and data analytics (more to come)

10. Advanced sampling methods and energy-landscape simulations (more to come)

11. Absolute binding free energy calculations (more to come)