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Molmodel Workshop. March 21, 2008 Christopher Bruns. Schedule. 8:30-10:00 Molmodel examples 10:00-10:15 Break 10:15-11:30 More Molmodel examples 11:30 Lunch 12:00 Your projects. What is Molmodel?. Domain-specific modeling layer on Simbody Part of SimTK core libraries

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molmodel workshop

Molmodel Workshop

March 21, 2008

Christopher Bruns

  • 8:30-10:00 Molmodel examples
  • 10:00-10:15 Break
  • 10:15-11:30 More Molmodel examples
  • 11:30 Lunch
  • 12:00 Your projects
what is molmodel
What is Molmodel?

Domain-specific modeling layer on Simbody

Part of SimTK core libraries

You should have Programmer’s Guide


Principal SimTK Core Libraries

SimTK Molmodel

molecular modeling

order(n) multibody


SimTK Simbody

numerical methods

and linear algebra

SimTK Math

SimTK Common

Vector, Matrix classes

and other data structures

SimTK Lapack

linear algebra

molecular physical units
Molecular Physical Units
  • Length: nanometers (10-9 meters)
  • Time: picoseconds (10-12 seconds)
  • Mass: atomic mass units (1/(Avogado’sConstant) grams)
  • Inert “noble” gas
  • Has no chemistry
  • van der Waals forces only
molecular force field
Molecular Force Field
  • What is a molecular force field?
    • A specification of all forces affecting a dynamic simulation. For conventional molecular simulation this includes non-bonded electrostatic forces and van der Waals forces, and bonded stretch, bend, torsion, and improper torsion parameters

Bridge between structural model and force field implementation

Concept borrowed from TINKER molecular dynamics package

argon exercises
Argon Exercises

Compile and run TwoArgons example program

Add a third argon atom.

What happens when atoms start too close together? Too far apart?

Increase the attractive force between atoms ten-fold

  • Two carbons, six hydrogens
  • One dihedral degree of freedom
  • 3 kcal/mol energy barrier to rotation
internal coordinates
Internal coordinates
  • Instead of explicit Cartesian X, Y, Z coordinates for an atom
  • Given three other atom positions, one distance, one bond angle, and one dihedral angle

1 distance



3 dihedral angle

bond angle 2



molecule internal coordinates
Molecule internal coordinates

Bond lengths, bond angles, dihedral angles

Mandatory for Compound construction

Optional for Compound simulation

ethane exercises
Ethane Exercises

Compile and run TwoEthanes example program

Add a third ethane molecule

macromolecules residues and atoms
Macromolecules, residues, and atoms
  • RNA, DNA, and protein are large molecules called macromolecules
  • Macromolecules consist of chains of residues





top level api for constructing proteins
Top level API for constructing proteins

#include “SimTKmolmodel.h”


simple protein
Simple protein
  • Construct protein from sequence
  • All atom parameters are built into AMBER99 force field
  • Note end caps
protein exercises
Protein Exercises

Compile and run SimpleProtein example program

Try a different sequence

Add a second protein

simple rna
Simple RNA
  • RNA from sequence
  • Writing PDB files
rna exercises
RNA Exercises

Compile and run SimpleRNA example program

Try a different sequence

Change the frequency of PDB writing

pdb the protein data bank
PDB: The Protein Data Bank
  • Repository of DNA, RNA, and protein atomic structures
  • Contains experimental results, not perfect models
  • Entries identified by 4 character ID, e.g. “1MRP”, “1GRZ”
  • Use “advanced search” at PDB web site to find structures.
pdb file format
PDB File format
  • Text format – humans can read it too
  • Most of the information is atomic coordinates
  • PDB files usually contain multiple molecules, including water molecules

ATOM 1751 N GLY C 250 32.286 1.882 43.206 1.00 22.00

ATOM 1752 CA GLY C 250 32.365 1.086 41.969 1.00 21.39

ATOM 1753 C GLY C 250 31.538 1.735 40.864 1.00 20.79

ATOM 1754 O GLY C 250 30.621 2.527 41.152 1.00 21.58

loadpdb exercises
LoadPdb Exercises

Download 1AKG from Protein Data Bank

Simulate 1AKG using Example

coarse grained representations in biology
Coarse-grained representations in biology

Natural lump sizes:

  • atoms
  • residues
  • base pairs
  • duplexes, alpha helices, beta strands
  • macromolecules
  • molecular assemblies
  • organelles
  • cells
  • tissues
  • organs
  • limbs
  • organisms
  • societies
  • ecosystems
  • biospheres
  • intergalactic federations

(picometer to micron scale)

(micron to mega-light-year scale)

coarse grained simulation of atom based molecular models
Coarse-grained simulation of atom-based molecular models
  • Full atom force field
  • coarse-grained motion permits longer integration time steps
  • Increasing coarseness
    • full Cartesian
    • torsion only (internal coordinate)
    • full rigid
molecule mobility partitioning
Molecule Mobility/Partitioning
  • What is molecule partitioning?
    • defining the movable degrees of freedom that will be used in a molecule simulation
  • Examples of partitioning strategies
    • Internal coordinates (fixed bond lengths and fixed bond angles)
    • Full Cartesian (conventional molecular dynamics)
    • Rigid molecules
rigidprotein exercises
RigidProtein Exercises
  • Simulate rigid protein
  • Create second protein
  • Convert to full Cartesian model
  • Which way is faster?
custom molecule construction
Custom Molecule Construction
  • BondCenters, Atoms, Bonds, Compounds
  • Inboard bond center
  • The first few atoms
  • Ring closing bonds
molecule construction nomenclature
Molecule Construction nomenclature

1: Atoms(3)

2: BondCenters(9)

3: Bonds(2)

4: Compound(1)