1. Ewald summation equations
2. Some interesting links
3. MD code written in C++
3. This section gives the details of the code that I developed during my PhD for Molecular Dynamics Simulation. Currently the code is not open source and used only for the MREL use.
Molecular Dynamics (MD) code in C++
1. Molecules supported currently
a) Argon, b) Platinum, c) Water SPCE rigid and d) SPCFw flexible
2) Force fields supported
a) Shifted Coulomb Potential
b) Lennard Jones (LJ) Potential
c) Zhu-Philpott (ZP) Potential
d) Spohr Potential
e) Harmonic Bond and Angle
3) Long Range force calculation modules
a) Classical Ewald summation
b) Smooth Particle Mesh Ewald (SPME)
c) Particle-Particle Particle Mesh (P3M)
4) Integrators
a) Velocity Verlet
5) Thermostats
a) Berendsen thermostat
b) Velocity scaling thermostat
c) Nose-Hoover thermostat
6) Boundary Conditions
a) xyz periodic
b) xy periodic, z walls
c) xy periodic, z- wall, z+ mirror
7) Pressure calculation
a) Irving Kirkwood
b) Standard virial based
c) Hardy's version
8) Additional modules implemented
a) Argon - Platinum heating model
b) Water - Platinum heating model
c) surface tension estimation
a) Argon, b) Platinum, c) Water SPCE rigid and d) SPCFw flexible
2) Force fields supported
a) Shifted Coulomb Potential
b) Lennard Jones (LJ) Potential
c) Zhu-Philpott (ZP) Potential
d) Spohr Potential
e) Harmonic Bond and Angle
3) Long Range force calculation modules
a) Classical Ewald summation
b) Smooth Particle Mesh Ewald (SPME)
c) Particle-Particle Particle Mesh (P3M)
4) Integrators
a) Velocity Verlet
5) Thermostats
a) Berendsen thermostat
b) Velocity scaling thermostat
c) Nose-Hoover thermostat
6) Boundary Conditions
a) xyz periodic
b) xy periodic, z walls
c) xy periodic, z- wall, z+ mirror
7) Pressure calculation
a) Irving Kirkwood
b) Standard virial based
c) Hardy's version
8) Additional modules implemented
a) Argon - Platinum heating model
b) Water - Platinum heating model
c) surface tension estimation
Placeholder for LJ potential parameters --For my internal use, use at your own risk
1. Argon-Argon interaction
\[\color{black} {\sigma_{Ar-Ar}=0.34 nm}\]
\[\color{black} {\epsilon_{Ar-Ar}=1.6567782\times10^{-21} J}\]
1 kJ/mol (0.23838 kcal/mol)
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2. Argon-Platinum interaction
\[\color{black} {\sigma_{Ar-Pt}=0.3085 nm}\]
\[\color{black} {\epsilon_{Ar-Pt}=8.94127465\times 10^{-22} J}\]
0.54 kJ/mol (0.128649 kcal/mol)
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3. Xenon-Xenon interaction
\[\color{black} {\sigma_{Xe-Xe}=0.4 nm}\]
\[\color{black} {\epsilon_{Xe-Xe}=3.14787864\times10^{-21} J}\]
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4. Water-Water SPCE
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5. Water-Platinum ZP potential
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\[\color{black} {\sigma_{O-O}=0.3166 nm}\]
\[\color{black} {\epsilon_{O-O}=1.0793\times 10^{-21} J}\]
\[\color{black} {q_{O}=-0.8476 e}\]
\[\color{black} {q_{H}=+0.4238 e}\]
0.65 kJ/mol (0.155291 kcal/mol)
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Unit Conversion
1 J/m = 1 N
1 kcal = 4.184 kJ
1 kcal/mol/A = 69.467 pN
1 kcal = 4.184 kJ
1 kcal/mol/A = 69.467 pN