NH Generalized Order Parameter

Calculates the generalized order parameter using the autocorrelation function of the NH vectors (requires well-fitted trajectory) or using the iRED procedure applied to the NH vectors.

Autocorrelation

$$C_f(j\Delta t) = \frac{1}{M}\sum_{i=0}^{N-1-M} f(i\Delta t)f((i+j)\Delta t)$$

python nh_order.py protein.tpr protein_nj_fit.xtc 5000 10000 "name N and not resname PRO and not resid 1" "name H and not resname PRO and not resid 1" 2 ./data/ --mode 0 --lenacf 100

$$C_f(j\Delta t) = \frac{1}{k}\sum_{i=0}^{k-1} f(iM\Delta t)f((iM+j)\Delta t)$$

python nh_order.py protein.tpr protein_nj_fit.xtc 5000 10000 "name N and not resname PRO and not resid 1" "name H and not resname PRO and not resid 1" 2 ./data/ --mode 1 --lenacf 100

iRED

python nh_order.py protein.tpr protein_nj_fit.xtc 5000 10000 "name N and not resname PRO and not resid 1" "name H and not resname PRO and not resid 1" 2 ./data/ --mode 2

Order parameter

Order parameter to any axis useful for membranes

python nh_order.py mem.tpr mem_mol.xtc 5000 10000 "name C3" "name H3" 2 ./data/ --mode 3 --vec 0 0 1