Master official page at Universitat Pompeu Fabra

Molecular simulations

Master project proposals 2011 in our group are available here ProjectProposalsMScBioinformatics2011.pdf.
The VMD exercise was done more or less equally well by all of you. I have given marks to Jordi.

Resources

You must install VMD 1.8.7 and NAMD2.7 for your architecture.
VMD user guide http://www.ks.uiuc.edu/Research/vmd/current/ug.pdf
ACEMD user guide http://multiscalelab.org/acemd/manual
Nice books:
- Computer Simulation of Liquids, Allen and Tildesley.
- Understanding Molecular Simulation, Second Edition: From Algorithms to Applications, Frenkel and Smit.

Classes 2011

Class 1: Molecular dynamics hands-on
- Concept of classical dynamics
- The water molecule
- Amber and Charmm forcefields (bond, angle, dihedral, improper, Lennard-Jones, Coulomb)
- Charmm topology filestop_all27_prot_lipid.top
- Charmm parameter filespar_all27_prot_lipid.prm
- Molecular dynamics codes
Class 2: Introduction to VMD
- http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/ (tutorial files http://www.ks.uiuc.edu/Training/Tutorials/vmd/)
- Use of the user guide http://www.ks.uiuc.edu/Research/vmd/current/ug.pdf (PDF), http://www.ks.uiuc.edu/Research/vmd/current/ug/ (HTML)
- Topics: Load molecule and navigate it, representations, selections (resname, name, type, resid), loading trajectories, keys (r,t,s,1,2,=) and tcl scripting (atomselect, measure)
- Exercises: VMD_exercise.txt
Class 3: Preparing a molecular structure for MD simulations
- Built from PDB in the Charmm format http://www.multiscalelab.org/acemd/protocols/ACETK.BLDCHARMM
- Relaxation and production run http://www.multiscalelab.org/acemd/protocols/ACETK.EQ
- Example of converting ACEMD input files to NAMD input.nve

#Example of converting ACEMD input files to NAMD
#comment restart on
#if there is not velocity file, add temperature 300 
#if present, comment hydrogenscale 4 and reduce timestep 2
...
#comment celldimension   68 66 56  
cellbasisvector1 68 0 0
cellbasisvector2 0  66 0
cellbasisvector3 0 0 56
...
paraTypeCharmm      on
...
#Add these lines if constraints is on
conskfile $structure.pdb
conskcol B
...
#comment energyfreq      1000
outputenergies      1000

Class 4: Free energy and steered molecular dynamics
- Slides: deca_alanine_FE.pdf (pending update)
- Required exercise files stretching.zip (based on the Stretching Deca-Alanine Tutorial)

Classes 2010

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)

Classes 2009

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

Note

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