(z[p][0] - y[p].dihedral(PHI)) +
FTSM.M(x[p], PHI, PSI) *
(z[p][1] - y[p].dihedral(PSI)))
z[p][1] -= (kappa / gamma) * dt * (FTSM.M(x[p], PSI, PHI) *
(zp0 - y[p].dihedral(PHI)) +
FTSM.M(x[p], PSI, PSI) *
(z[p][1] - y[p].dihedral(PSI)))
# UPDATE CARTESIAN
prop[p][0].propagate(scheme="velocityscale",
steps=1,
dt=dt,
forcefield=ff,
params={'T0': 300})
prop[p][1].propagate(scheme="velocityscale",
steps=1,
dt=dt,
forcefield=ff,
params={'T0': 300})
# My own function which sets phi and psi for individual force objects
# Saves performance since I only change 'angle', I don't want to define
# all new force objects by changing params.
#FTSM.setConstraint(phi=z[(p+1)%numpoints][0], psi=z[(p+1)%numpoints][1], kappa=kappa, forcefield=ff)
z = FTSM.reparam(z)
print "\nI" + str(iter + 1) + ": ", z
#io.plotVector(prop[0][0],stringgraph,z, rangex=[-numpy.pi, numpy.pi], rangey=[-numpy.pi, numpy.pi])
kappa += (100.-40.)/90000.
if (p != 0 or iter != 0):
FTSM.setConstraint(PHI, PSI, phi=z[p][0], psi=z[p][1], kappa=kappa, forcefield=ff)
# UPDATE FREE SPACE
# USE FIRST SYSTEM TO GET M
# USE SECOND SYSTEM TO OBTAIN PHI AND PSI DIFFERENCES
# FROM TARGETS
zp0 = z[p][0]
z[p][0] -= (kappa/gamma)*dt*(FTSM.M(x[p], PHI, PHI)*(z[p][0]-y[p].dihedral(PHI)) + FTSM.M(x[p], PHI, PSI)*(z[p][1] - y[p].dihedral(PSI)))
z[p][1] -= (kappa/gamma)*dt*(FTSM.M(x[p], PSI, PHI)*(zp0-y[p].dihedral(PHI)) + FTSM.M(x[p], PSI, PSI)*(z[p][1] - y[p].dihedral(PSI)))
# UPDATE CARTESIAN
prop[p][0].propagate(scheme="velocityscale", steps=1, dt=dt, forcefield=ff, params={'T0':300})
prop[p][1].propagate(scheme="velocityscale", steps=1, dt=dt, forcefield=ff, params={'T0':300})
# My own function which sets phi and psi for individual force objects
# Saves performance since I only change 'angle', I don't want to define
# all new force objects by changing params.
#FTSM.setConstraint(phi=z[(p+1)%numpoints][0], psi=z[(p+1)%numpoints][1], kappa=kappa, forcefield=ff)
z = FTSM.reparam(z)
print "\nI"+str(iter+1)+": ",z
#io.plotVector(prop[0][0],stringgraph,z, rangex=[-numpy.pi, numpy.pi], rangey=[-numpy.pi, numpy.pi])
