Comparative Study of NAMD and GROMACS

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Comparative Study of NAMD and GROMACS

• Yanbin Wu, Joonho Lee and Yi Wang
• Team Project for Phy466
• May 11, 2007

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Outline

• Motivation
• Simulation Set-up
• Procedure
• Result and analysis
• Conclusion

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Motivation (1)

• NAMD and GROMACS
• GROMACS
• developed in the Netherlands.
• Fast, free.
• NAMD
• developed in Urbana, IL.
• Parallel, fast for big systems, free.

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Motivation (2)

• Compare two packages
• Both are widely used MD packages.
• Different code implementation in the two packages
  may cause different results
• Generally, one group mainly uses one package
• Good chance to compare two packages !!!

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Simulation Setup (1)
running parameter
Implementation
Simulation Package
RESULTS
model (topological)
force field
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Simulation Setup (2)

• Algorithm
• Running parameter
• Initial system
• Size, composition
• Coordinate, velocity
• Force field
• LJ parameter
• Model
• Charge, bonding, angle parameter
• Code implementation
• Black box

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Procedure

• Find a zero point
• NVE
• NVT
• Compare different water models
• TIP3P
• SPCE
• Compare different temperature control schemes
• Langevin
• Nose Hoover
• Berendsen

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Simulation system

• The simplest system
• Water
• Solvent of life
• Simple isotropic
• Rich in experimental data
• WaterIons
• Ensembles
• NVE
• NVT
• Langevin, Nose-hoover, Berendsen

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Water Model SPCE

• SPC/E rigid model (Berendsen et al., 1987)
• q(h) 0.4238, q(O) - 0.8476
• O-H distance 1 (Å)
• H-O-H angle 109.47
• LJ parameter
• A 0.37122(kJ/mol)1/6.nm and B 0.3428
  (kJ/mol)1/12.nm

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Water Model TIP3P

• TIP3P flexible model (Mahoney and Jorgensen,
  2000)
• q(h) 0.417, q(O) - 0.834
• O-H distance 0.9572 (Å)
• H-O-H angle 104.52
• LJ parameter
• 0.1521, 3.15061(Å)

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Temperature control schemes

• Langevin
• Introduce a random force and friction coefficient
• Nose-hoover
• Introduce a thermal reservoir and a friction term
  in the eq. of motion
• Berendsen
• Weak coupling first-order kinetics to an external
  heath bath with a given temperature

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Results and Analysis (1)

• Zero point
• NVE
• 0.25 ns NVT to bring temperature up to 300K.
• 1 ns NVE.
• Important start with the same velocity and
  coordinate in both packages.
• NVT
• 1 ns NVT using Langevin dynamics temperature
  control, damping coefficient 5/ps.

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NVE Zero Point
5.6 difference
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NVT Zero Point
7.3 difference
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Results and Analysis (2)

• Different water models
• 1 ns NVT using Langevin dynamics with ? 5/ps.
• Two different water models SPCE and TIP3P.
• Most commonly used water models.
• SPCE and TIP3P water models exhibit similar
  dynamic properties in GROMACS.

0.032 difference
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Results and Analysis (3)

• Damping in Langevin Dynamics
• 1 ns NVT via Langevin dynamics with ? 1, 5, 10
  /ps.
• Damping affects the diffusion of water
  dramatically.
• ?5/ps best reproduces the experimental result.

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Results and Analysis (4)

• Different temperature control schemes
• 1 ns NVT using Langevin dynamics with ? 5/ps
• 1 ns NVT using Nose-hoover thermostat with ?0.1
  ps
• 1 ns NVT using Berendsen thermostat with ?0.1 ps
• Different temperature control schemes can
  achieve similar results with well-chosen
  parameters.

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Results and Analysis (5)

• Water in the waterion system

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Results and Analysis (5)

• Na in the waterion system

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Results and Analysis (5)

• Cl- in the waterion system

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Results and Analysis (5)

• Radial distribution of oxygen - oxygen

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Results and Analysis (5)

• Radial distribution of oxygen Cl-

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Results and Analysis (5)

• Radial distribution of oxygen Na

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Conclusion

• The two packages GROMACS and NAMD produce similar
  results (within tolerance) using the same set of
  parameters.
• Damping coefficient affects the dynamics
  significantly and has to be chosen with caution.
• Different temperature control schemes may
  generate similar dynamic properties.
• Two different water models, SPCE and TIP3P were
  compared and only minor difference was observed
  regarding the diffusion of water.

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Discussion

• Energy conservation in NVE simulations
• Neighbor list update frequency
• Switch or shift function is required, instead of
  cutoff
• PME
• Damping coefficient in NVT simulations
• Balance temperature fluctuation and disturbance
  to the motion of the system.
• Different temperature control schemes

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Zero point (waterion, NVT)
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Water Model (3)
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NVE Zero Point