CoSIMS

CoSIMS is a Collision Simulator for Ion Mobility Spectrometry. This is a trajectory based method for calculating molecular colision cross-sections for use with IMS-MS experiments. We welcome the submission of bugs, improvements, and suggestions to the code.

If you find this code usefull, we ask that you please cite the following paper:

Christopher A. Myers, Rebecca J. D’Esposito, Daniele Fabris, Srivathsan V. Ranganathan, and Alan A. Chen. CoSIMS: An Optimized Trajectory Based Collision Simulator for Ion Mobility Spectrometry. J. Phys. Chem. B., May 2019, 10.1021/acs.jpcb.9b01018. https://pubs.acs.org/doi/10.1021/acs.jpcb.9b01018

Installation

Obtaining the Code

To obtain the program from the GitHub repository:

git clone https://github.com/ChristopherAMyers/CoSIMS.git

Alternatively, download the .zip file from GitHub and extract the contents manually.

Building

• Requirements:
  • g++ version 4.8.1 or higher
  • OpenMP library for multi-threading
  • Linux system (Windows not tested)

To build the program:

make

Or compile using multiple cores:

make -j

This creates a statically linked binary at:

/path/to/cosims/install/bin/cosims

Manual compilation:

g++ src/*.cpp -o cosims -std=c++11 -fopenmp -O3

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Running CoSIMS

Basic run command:

./cosims -m moleculeFile.xxx

Where xxx = pdb or mfj.

Additional options:

./cosims -m moleculeFile.xxx -[option] [value]

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Molecule File Types

PDB Files

• Uses ATOM and HETATM entries.
• Assumes all entries belong to one structure.
• Columns 78–79 specify element types; if blank, atom name columns 13–16 are used.

Example:

ATOM      1  OH5’ C5       1       3.429  -7.861   3.641  1.00  0.00  H

MFJ Files

• Follows MOBCAL syntax with added integer charge support.

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Random Seed

Set with -s option:

./cosims -m file.pdb -s 12345

Uses 64-bit Mersenne Twister RNG.
Same seed may yield different results with multiple threads due to dynamic allocation.

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Number of Threads

Set with -n option:

./cosims -m file.pdb -n 4

• Should be ≤ number of physical CPU cores.
• Identical runs may produce different results due to thread-safe RNG.

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Atom Types

Set with -a option to provide custom parameters.
Format:

#name  symbol  mass   sigma    epsilon    intMass
Carbon C       12.010 2.043    0.03090114 12
Hydrogen H      1.008 2.043    0.01498936 1

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Input File

Use -i option for runtime configuration without recompiling.

Example input file:

# CoSIMS input file
name myName
dt 0.01
temp 298
traj 50
iter 15
threads 1
seed 12345
dispersion cutoff true
dispersion radius 40
multipole true
multipole order 1

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Available Program Options

Option	Description	Type	Default
name	Project name / output file prefix	string	log charge
dt	Verlet integration time step (ps)	float	0.01
temp	Temperature (K)	float	298
traj	Trajectories per CCS integral (×10³)	int	50
iter	Number of CCS integrals to average	int	10
print rate	Print CCS progress every N trajectories	int	20000
print mol	Print rotated molecule to XYZ	bool	false
dir	Output directory	string	Current directory
charge	Uniform total charge (e)	int	0
threads	OpenMP threads (overrides -n)	int	1
seed	RNG seed (overrides -s)	int64	random device()
dispersion cutoff	LJ cutoff enabled	bool	true
dispersion radius	LJ cutoff radius (Å)	float	Based on vdW radii
multipole	Enable multipole approximation	bool	false
multipole radius	Radius for multipole approximation (Å)	float	20.0
multipole order	0 = monopole, 1 = dipole, 2 = quadrupole	int	1
max cluster size	Max radial distance for atom clusters	float	4.0

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References

1. M. F. Mesleh et al., The Journal of Physical Chemistry, 100(40):16082–16086, 1996.
2. A. A. Shvartsburg, M. F. Jarrold, Chemical Physics Letters, 261(1):86–91, 1996.