Molecular simulations

alt Universitat Pompeu Fabra

Requirements

You must install VMD 1.8.6 and NAMD2.6 for your architecture.

Class 1: Introduction to VMD
- http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/vmd-tutorial-2009.html
Class 2: PDB manipulation and generation of PSF
- Slides: msi_class_2_2010.pdf
Class 3: Running a simulation
- Concept of classical dynamics
- The water molecule
- Forcefields (bond, angle, dihedral, improper, Lennard-Jones, Coulomb)
- Charmm topology filestop_all27_prot_lipid.top
- Charmm parameter filespar_all27_prot_lipid.prm
- NAMD equilibration script: run.namd
Class 4: Visualization and analysis with VMD
- Use of the user guide http://www.ks.uiuc.edu/Research/vmd/current/ug.pdf
- Hot keys and pick modes
- selection (resname, name, resid (not residue), type, ...)
- Exercises: EXERCISE_VMD.txt
- TRJ: http://www.gpugrid.net/download/trj.dcd
- PDB: http://www.gpugrid.net/download/TIM_sub_cry.pdb
Class 5: Free energy and steered molecular dynamics
- Slides: deca_alanine_FE.pdf
- Required exercise files stretching.zip (based on the Stretching Deca-Alanine Tutorial)

For the test, provide the VMD scripts resolving over the PDB 1NEY :

a) Determine all residues within 5A of GLU165 of chain A.

b) What is the distance between C-alphas of GLU165 and ILE92 of chain A

c) Determine the three closest aminoacids of the oxigens with name OE1 OE2 of GLU165

d) Compute the minimum distance of contacts of two Tyr at the dimer interface

e) Count the number C-alphas of aminoacids within 6A of ILE92 of chain A

by 22th March. Send the scripts to gianni.defabritiis@upf.edu

Class 1: Introduction to classical molecular dynamics
- Concept of classical dynamics
- The water molecule
- Forcefields (bond, angle, dihedral, improper, Lennard-Jones, Coulomb)
- Charmm topology filestop_all27_prot_lipid.top
- Charmm parameter filespar_all27_prot_lipid.prm
- Exercise: Write the Argon topology and parameter files
Class 2: Setting up an Argon simulation
- http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/index.html (tutorial files http://www.ks.uiuc.edu/Training/Tutorials/vmd/)
- Argon box argon0.pdb.gz create_psf.tcl (use your argon top and par files)
- Exercise: Equilibration of Argon with NAMD and analysis of g(r) minimize_argon.conf, thermalise.conf
Class 3: VMD for analyzing a molecular system
- argon_eq.coor
- Argon phase diagram http://media-2.web.britannica.com/eb-media/95/2395-004-4F69A001.gif
Class 4: VMD/NAMD setup and equilibrate a globular protein
- PDB 1NEY: 1NEY.pdb
- psfgen create script: create_TIM.tcl. psfgen user manual: www.ks.uiuc.edu/Research/vmd/plugins/psfgen/ug.pdf
- NAMD equilibration script: run.namd
Class 5: Visualization and analysis with VMD
- Use of the user guide http://www.ks.uiuc.edu/Research/vmd/current/ug.pdf
- Visualization modes (VDW, CPK, Surf, coloring, trasparency)
- Hot keys and pick modes
- selection (resname, name, resid (not residue), type, ...)
- Exercises: EXERCISE_VMD.txt

If the newcartoon representation does not work under Linux, try to set export VMDSIMPLEGRAPHICS=1.