A minim example of visco-elasticity calculation based on openmm (need some additional packages: numpy, openmm=8.4);
Main file: rerun_sTen_t100.py
PDB file: 'start.pdb'
Simulation sets saved in 'start_system.xml', 'start_integrator.xml' and 'start_state.xml' Stress tensor reporter: 'pressurereporter.py'
Generate stress tensor file 'start_sTens.out' for the following visco-elasticity calculation.
Generate log file 'start_state.log'
Trajectory recorder can be added to generate trajectory
Calculation for viscosity, viscous and elastic moduli of condensate Gradual calculation for relaxation modules G(t), viscosity, G'(w) and G"(w) by multi-timescale method.
The cutoff time needs to be set (usually the variable "ind1=100")