Download Molecular Dynamics Simulation Program MARBLE User`s Manual

3.Tutorials
[nonbond]
cutoff = 10.0
[ewald]
d_grid = 1.1
[PT_control]
ensemble = NPT
temperature = 300
method = extended_system
initialize = on
[constraint]
rigid_body = hydrogen
[md]
time_step = 2.0
step = 5000000
print_step = 100
trj_file = 193L_w-run01.trj
trj_step = 500
prop_file = 193L_w-run01.prop
prop_step = 50
[output]
crd_file = 193L_w-run01.crd
pdb_file = 193L_w-run01.pdb
For the MARBLE input files, specify the parameters under each section indicated with "[ ]". For details
on the input file contents, see the chapters with the descriptions.
[PT-control]
 ensemble = NPT
Specifies the system ensemble to NPT.
 method = extended_system
Controls the temperature in the nose-hoover method. If "method" is not specified, the
extended_system is set as the default method.
 initialize = on
Initializes the parameters for NPT. This setting will be canceled in later calculations to inherit the NPT
ensemble data in the input crd file.
3.3.2.2. Targeted MD of the transition from closed to open conformation of F1 motor
Targeted MD reproduces conformation change of proteins much faster than the actual time scale by
applying force to the proteins atoms to promote the change. The following shows the input file of the productive
run applying the force to theβ-subunit atoms of F1 motor.
Productive run
The productive run of the Targeted MD is performed using the coordinate of the system after the
equilibration is complete. This example calculates the transition from closed to open conformation of the
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