MM4

Molecular Mechanics force field, version 4. The simulator used to create Nanosystems (1992), but updated with modern ab initio parameters.

Documentation: philipturner.github.io/MM4

Supported Parameters

Atoms:

Element	Ring Types
H	n/a
C	5, 6
Si	5, 6
P	5, 6
S	5, 6
Ge	5, 6

Bonds:

Element	H	C	Si	Ge
C	X	X	X	X
Si	X	X	X
P		X
S		X
Ge	X	X		X

Forces:

• bend
• external
• nonbonded
  • van der Waals force
  • overlap repulsion
  • electrostatic force
• stretch
• stretch-bend

Levels of Theory

MM4 currently offloads molecular dynamics calculations to OpenMM. Rigid body dynamics must be integrated on the CPU by the library user. Any communication between CPU and GPU causes a latency bottleneck. This bottleneck manifests as a large $O(1)$ term in the polynomial for algorithmic complexity.

	Stable Time Step	Minimum Latency/Step	Maximum ns/day	Scaling	Force Computation	Integration
Molecular Dynamics (no cutoff)	2.5 fs	175 μs	1250 ns/day	$O(n^2)$	GPU	GPU
Molecular Dynamics	2.5 fs	375 μs	550 ns/day	$O(n)$	GPU	GPU
Rigid Body Dynamics	80 fs	1500 μs	4000 ns/day	$O(n)$	GPU	CPU

For large atom counts and lower-end hardware, the $O(n)$ term will dominate. This term is around the compute cost of biomolecular force fields (e.g. AMBER). However, GPU hardware allows several thousand calculations to occur each clock cycle. This fact makes MM4 much faster than CPU-based simulators (GROMACS, LAMMPS) running the same type of force field.

There is currently a massive bottleneck in the $O(n)$ term for nonbonded forces. It makes MM4 roughly 3x slower than it should be. The current performance of MM4 w/ GPU could equate to GROMACS w/ CPU, until the bottleneck is fixed.

Explained in more detail here: openmm/openmm#5095

Units

MM4 and OpenMM use slightly different unit systems. MM4 adheres to the SI system: nanometer, yoctogram, picosecond. Units for force and energy are derived from dimensional analysis.

energy = m * v^2 = yg * (nm/ps)^2 = zJ
force = dU / dx = zJ / nm = pN

Unit	MM4	OpenMM
Angle	rad	rad
Energy	zJ	kJ/mol
Force	pN	kJ/mol/nm
Mass	yg	amu
Length	nm	nm
Speed	nm/ps	nm/ps
Time	ps	ps

Value in SI Units	SI Unit	MM4	OpenMM
Angle	rad	1	1
Energy	J	1e-21	1.66e-21
Force	N	1e-12	1.66e-12
Mass	kg	1e-27	1.66e-27
Length	m	1e-9	1e-9
Speed	m/s	1000	1000
Time	s	1e-12	1e-12

Reproducible Windows Testing

Download Anaconda

• Start with this link: https://www.anaconda.com/download
• Under Free Download, click Skip registration
• Choose Miniconda Installers and not Distribution Installers
• Install the Windows 64-Bit Graphical Installer
• Press the Windows key on the keyboard, opening up Type here to search. Open Anaconda Prompt, not Miniforge Prompt.
• In the Anaconda terminal, type conda install -c conda-forge openmm

Move binaries into repo directory

• In the File Manager, locate "/C:/Users/<your username>/miniconda3/Library/lib"
• Copy the files OpenMM.dll and OpenMM.lib into the cloned MM4 repo

Purge Anaconda OpenMM for reproducibility

• In the Anaconda terminal, type conda uninstall openmm

Now, run ./test.bat in the VS Code terminal.