Convert trajectory of normal modes to nmd format for visualizing with NMWiz

convert_Universe_to_nmd.py

def convert_univ_to_nmd(u, nmd_name, title='generic_title'):
    """
    Convert MDAnalysis.Universe normal mode trajectory to nmd format
    
    u should be a MDAnalysis.Universe with each frame of the trajectory
    being the cartesian displacements for a single normal mode.
    For example, the trajectory written by the nmeig tool of GROMACS
    (http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-nmeig.html)
    gives an appropriate trajectory with the -v option.
    The file written with nmd_name will be in the nmd format that
    can be read by the NMWiz plugin to VMD 
    (https://www.ks.uiuc.edu/Research/vmd/plugins/nmwiz/).
    """
    with open(nmd_name, 'w') as f_out:
        w = f_out.write
        w(f'title {title}\nnames')
        for a in u.atoms:
            w(f' {a.name}')
        w('\nresnames ')
        for a in u.atoms:
            w(f' {a.resname}')
        w('\nresnums ')
        for a in u.atoms:
            w(f' {a.resid}')
        w('\nchids ')
        for a in u.atoms:
            w(f' {a.segid}')
        w('\ncoordinates ')
        u.trajectory[0]
        for a in u.atoms:
            pos = a.position
            w(f' {pos[0]} {pos[1]} {pos[2]}')
        for i in range(1, len(u.trajectory)):
            u.trajectory[i]
            inv_freq = 1. / np.sqrt(u.trajectory.time)
            inv_freq = inv_freq if not np.isnan(inv_freq) else 1.
            w(f'\nmode {i} {inv_freq} ')
            for a in u.atoms:
                pos = a.position
                w(f' {pos[0]} {pos[1]} {pos[2]}')