Using Molecular Dynamics Code

1
Using Molecular Dynamics Code

• Current version 3.0
• Chakravarthy Ayyagari
• Dmitry Bedrov
• Grant D. Smith

2
Bridging between theory and results

• Theory(Force field, Newtons eqns of motion,
  different electrostatics, etc.)
• Code
• Results (Validation with experiments, property
  evaluation, etc.)

3
The Code

• Input
• fort.11
• fort.12
• fort.25
• fort.26

• Output
• fort.66
• fort.65
• fort.77
• fort.78
• fort.76
• fort.59

4
Description of input files

• fort.11- Molecular description ( number of
  molecules, free ions, bonds, bends,torsions,deform
  ations for each chain, connectivity
• fort.12 - Force field parameters - Valence, bend,
  dihedral and out-of-plane parameters, non-bonded
  LJ/E6 parameters
• fort.25- Parameters involved in a run- Number of
  integration steps, timestep, cutoff, ensemble,
  etc.
• fort.26- The initial coordinates and velocities
  for the run, atom labels, charge description
• fort.65 - The averaged properties with a
  pre-defined frequency, final values for the
  entire run
• fort.66 - Final coordinates and velocities in the
  format of fort.26
• fort.59 - Averaged non bonded energy split (
  inter-molecular and intra-molecular)
• fort.77 - Binary output of coordinates for
  further analyses
• fort.78 - Binary output of stress tensor for
  further analyses
• fort.76 - Binary output of charge flux, box
  dipole for further analyses.

5
Fort.12
6
Fort.25
7
Fort.11
8
Fort.26
9
Restrictions in current version

• Bond numbering
• The second atom should have a higher atom number
• Chain consistency
• Non-bonded interaction distance should not go
  below one Angstrom