This repository demonstrates how to use ManyAngle.cpp with urea simulation produced by Pablo M. Piaggi and Michele Parrinello in this paper. The simulation files including inputParameters.mdp, melt450K-B.gro, topol.top, and centers.dat are taken from Pablo Piaggi. For more details, please refer to his github or website, or email him directly.

How to perform simulation

sh createTpr.sh // This will generate md.tpr
gmx_mpi mdrun -deffnm md -plumed plumed_many.dat -cpi md.cpt

The plumed_many.dat will compile ManyAngle.cpp and generate ManyAngle.o & ManyAngle.so. At the same time, this plumed file will also generate COLVAR and HILLS files with metadynamics adding bias as function of two angles calculated by the ManyAngle.cpp.

Note

getPosition(0): x_0

getPosition(1): y_0

getPosition(2): z_0

getPosition(3): x_1

...

• The original ManyAngle2_ST.cpp doesn't consider pbc when calculating molecular vectors.
• Since our manyangle op need other thresold for complementary angles, we also remove up-down symmetry flag in ManyAngle.cpp.
• There is no significant difference with/without low comm, so we also remove it in ManyAngle.cpp.