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NAMD and GROMACS
The Quest To Go Parallel
Peter SpijkerCalifornia Institute of Technology
Materials Process and Simulation CenterBiochemistry & Molecular Biophysics
Technische Universiteit EindhovenDepartment of Biomedical Engineering
Division of Biomedical Imaging and Modeling
March 2, 2004
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Presentation Overview
• Purpose of presentation
• NAMD? GROMACS? What the heck?
• Discussion on both packages
• Compare both packages
• Examples
• Parameter files
• Parallelisation
• References
• Questions
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Purpose Of This Presentation
• Give a first glimpse on NAMD and GROMACS
• A (very) short introduction how to use them
• Explain reasons for using this packages
• Discuss the parallel -experience
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NAMD? GROMACS? What The Heck?
• NAMD is short for:
Not (just) A nother Molecular Dynamics Program
• Developed by the Theoretical Biophysics Group (Klaus Schulten) at the University of Illinois at Urbana-Champaign
• GROMACS is short for:
Groningen Machine for C hemical S imulations
• Developed by the Berendsen Group, Department of Biophysical Chemistry, University of Groningen, The Netherlands
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NAMD? GROMACS? What The Heck?
• Both packages are Molecular Dynamics Programs
• Both aimed for high-performance simulations
• Both are designed for parallel systems. This is a development of the last years.
• Both are pretty young (in their current form):
NAMD: 1999
GROMACS: 2001
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Molecular Dynamics
• A couple of remarks on Molecular Dynamics:
• Simulations are classical
• Electrons are in the ground state
• Force fields are approximate
• Force field is pair-additive
• Long range interactions are cut off
• Boundary conditions are unnatural
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NAMD
• A short overview:
• Force Field Compatibility (CHARMM & X-PLOR)
• Full Electrostatics (Particle Mesh Ewald)
• Multiple Time Stepping ( Verlet)
• Input and Output Compatibility (PDB & PSF & DCD à VMD)
• Dynamics Simulation Options (next slide)
• Easy to Modify and Extend (C++)
• Interactive MD Simulations
• Load Balancing
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NAMD
• Dynamics Simulation Options:
• Constant Energy Dynamics
• Constant Temperature Dynamics
• Periodic Boundary Conditions
• Constant Pressure Dynamics
• Energy Minimization
• Fixed Atoms
• Rigid Waters
• Rigid Bonds to Hydrogens
• Harmonic Restraints
• Spherical or Cylindrical Boundary Restraints
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NAMD
• Used forcefields
• CHARMM
• X-PLOR
• AMBER
• GROMACS
• But:
• Bond potentials are always approximated with harmonic or sinusoidal potentials
• For both AMBER and GROMACS restrictions apply
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GROMACS
• A short overview:
• Claimed being the fastest code in the world
• A good set of bonded and non-bonded interaction equations
• Long Range Electrostatics ( Ewald, PME, PPPM)
• All hydrogen forcefield
• Output compatibility (GRO à VMD)
• Possibility of Reduced Units with Lennard-Jones
• Simple forcefield files à Easy to do coarse grain
• Large Analysis Toolkit
• Easy to extend (C++)
• Uses preprocessor (GROMPP) to optimise the input files
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GROMACS
• Dynamics Simulation Options
• Shell Molecular Dynamics
• Constraint algorithms (SHAKE, LINCS)
• Simulated Annealing
• Stochastic Dynamics (Verlet)
• Brownian Dynamics (position Langevin)
• Energy Minimization (Steepest Descent, Conjugate Gradient)
• Normal Mode Analysis
• Free Energy Calculations
• Essential Dynamics Sampling (WHATIF)
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GROMACS
• Non-Bonded Interactions:
• Lennard-Jones
• Buckingham
• Coulomb interaction
• Coulomb interaction with reaction forcefield
• Modified non-bonded interactions (shift function, Ewald summation)
• Bonded Interactions:
• Bond Stretching Harmonic Potential
• Morse Potential Bond Stretching
• Cubic Bond Stretching Potential
• Harmonic Angle Potential
• Cosine based angle potential
• Improper and Proper dihedrals
• All type of restraints
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NAMD vs GROMACS
• Both packages are very useful
• Both perform well on parallel systems
• NAMD is more focussed on biological simulations (proteins, lipid bilayers)
• GROMACS is more aimed for computational chemistry on a whole
• Both are highly compatible with themselves and other programs for both analysing and visualisation
• GROMACS is very useful for coarse grain simulations
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Examples
• NAMD
• Apolipoprotein (benchmark)
• Bovine Pancreatic Trypsin Inhibitor (interactive)
• Alanine (small, isolated)
• GROMACS
• Dipalmitoylphosphatidylcholine (DPPC)
• Full Atomistic
• Coarse Grain
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Examples - NAMD
• Apolipoprotein (benchmark)
92.224 atoms, 1.0 ps, 300 K, periodic
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Examples - NAMD
• Bovine Pancreatic Trypsin Inhibitor (interactive)
822 atoms, 20 ps, 300 K, minimisation
Interactive :
- Watching
while running
- Possibility to
pull atoms to
a position
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Examples - NAMD
• Alanine
66 atoms, 10 ps, 300 K, free, runtime = 1.5 minutes
Show in VMD
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Examples - GROMACS
• Dipalmitoylphosphatidylcholine (DPPC, benchmark)
Full atomistic, 121.856 atoms, 10 ps, 323 K, periodic
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Examples - GROMACS
• Dipalmitoylphosphatidylcholine (DPPC)
Coarse Grain, 27.324 particles, 400 ps, 323 K, periodic
± 17 min on 1 proc.
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Forcefield file
• GROMACS Forcefield file
• Define Atomtypes
• Define Non-bond parameters
• Define Molecule Types
• Define Atoms
• Define Bonds, angles, dihedrals
• Define System
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Input- And Outputfiles
• NAMD:
Input:
• PDB: coordinate & velocity file
• PSF: structure file
• FF: CHARMM, X-PLOR parameter file
• NAMD: Simulation parameter file
Output:
• COOR: final coordinate file
• VEL: final velocity file
• DCD: trajectory file
• DAT: run information (energies and so on)
• XSC: System configuration output
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Input- And Outputfiles
• GROMACS:
Input:
• GRO: coordinate & velocity file
• TOP: topology (i.e. structure) of the system
• ITP: force field (can be included in TOP)
• MDP: simulation parameter file
Preprocessed:
• TPR: simulation input file
Output:
• GRO: final configuration & velocity file
• TRR/XTC: trajectory file
• EDR: energies
• LOG: run information
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The Quest To Go Parallel
• Why parallel?
• Longer simulations
• Larger systems
• More complex systems
• Keep in mind that communication can
be the bottle-neck
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Parallel Computation
• Basic idea is to run divide the work of the job throughout a number of processors
• Involves intelligent communication between processors to share information
• Using Batch Scripting to submit jobs
• Using MPI to communicate and build topology
BORG
NODE
HULK
NODE NODE
5
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The Power Of Parallel Computation
• Benchmark System NAMD
• Apolipoprotein
92.224 atoms
Full atomistic
Coulomb interactions
Explicit water
• Run information
1000 steps à 1.0 ps
• Computational time
1 processor: 1 hour 30 minutes à 16 ps/day à S = 100%
4 processors: 25 minutes à 57.6 ps/day à S = 90%
8 processors: 14 minutes à 102.9 ps/day à S = 80%
Computations performed on BORG
S = scaling on parallel system
S = per_N / ( N * per_1 )
per_x = picoseconds per day
N = number of nodes
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The Power Of Parallel Computation
• Benchmark System GROMACS
• Dipalmitoylphosphatidylcholine
121.856 atoms
Full atomistic
Coulomb interactions
Explicit water
• Run information
5000 steps à 10 ps
• Computational time
1 processor: 2 hour 30 minutes à 96 ps/day à S = 100%
5 processors: 36 minutes à 390 ps/day à S = 82%
8 processors: 29 minutes à 480 ps/day à S = 62%
Computations performed on BORG
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The Power Of Parallel Computation
• Coarse Grain System on GROMACS
• Dipalmitoylphosphatidylcholine
27.324 particles (± 110.000 atoms)
Coarse Grain
Coulomb interactions
Coarse grained water (1 particle)
• Run information
10.000 steps à 400 ps
• Computational time
1 processor: 17 minutes à 33.882 ps/day à S = 100%
4 processors: 9 minutes à 64.000 ps/day à S = 47%
Computations performed on BORG
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Conclusions
• NAMD & GROMACS are useful for Molecular Dynamics
• NAMD scales better in parallel performances
• GROMACS is faster in calculations (ps/day)
• Coarse Grain simulations are easy to perform
• Parallel simulations are easy to run
• Minor disadvantage: network data transfer
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References
• NAMD User Manual
• GROMACS User Manual
• NAMD website: http://www.ks.uiuc.edu/Research/namd
• GROMACS website: http://www.gromacs.org
• Brooks et al. CHARMM , J. Comp. Chem. (1982)
• Lindahl et al. GROMACS, J. Mol. Model. (2001)
• Marrink et al. CG Model, J. Phys. Chem. (2004)
• Manuals will be made available through website FF -group
• For information how to run: pspijker@wag.caltech.edu
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Further Questions
?
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