Running AWH with polymer end to end distance as the reaction coordinate

User discussions
1

GROMACS version:2021.5
GROMACS modification: No
Hello all,

I am hoping to run free energy calculations on a polymer crystal system using the end to end distance of the polymer as the reaction coordinate. The issue is that the polymer wraps around the periodic boundary conditions leading the end to end distance short even when the polymer is fully extended. Is there a way to use the end to end distance as given by gmx polystat (e.g. considering periodic boundaries) as the reaction coordinate for awh?

Thanks for any help

2

This is possible when you pull along one dimension, e.g. x, and fix the box dimension along that dimension. Then you can use pull-geometry=direction-periodic.