This fork of Gromacs modifies it to enable output of two-dimensional flow fields, collected during a simulation.

Follow the regular Gromacs installations instructions. While not required, it is recommended to set the cmake option -DGMX_VERSION_STRING_OF_FORK=flow-field.

The flow field collection uses the following MDP options:

; How often to sample the velocity field
userint1 = 40 

; How often to save the velocity field to disk
userint2 = 5000

; Number of bins along the x axis
userint3 = 200

; Number of bins along the z axis
userint4 = 100

; List of groups to collect data for
user1-grps = SOL ; water 

Additionally, mdrun needs to know where to save the output, for which the -flow option has been added:

$ gmx mdrun -flow maps/flow   # Saves to `maps/flow_00001.dat`, 
                              #          `maps/flow_00002.dat`,
                              #          `maps/flow_00003.dat`,
                              # etc.

• Can currently only sample data in the x-z plane.
• Temperature calculation is only correct for water
• Currently only works for static box size

Tools used to read and manipulate the created data is available in a Python 3 module. It is available in this repository:

https://github.com/pjohansson/gmx_flow_utils

These changes are distributed under the same terms as Gromacs. See COPYING for more information.