PeriodicBoxMover

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PeriodicBoxMover

This mover runs Monte Carlo (MC) simulation in isothermal-isobaric (NPT) condition on a periodic boundary box. Can be applied to a broad range of (small molecules) to extract their thermodynamic properties. Currently it has been applied to running liquid-state simulation of small molecules; see Park et al (2016), "Simultaneous optimization of biomolecular energy function on features from small molecules and macromolecules", JCTC. Details will be added more in near future.

<PeriodicBoxMover name=(&string) scorefxn=(&string)
                  nmol_side=(5 &Size) nsteps_equilibrate=(500000 &Size) nsteps_sim=(1000000 &Size) 
                  vol_step=(40.0 &Real) rot_step=(15.0 &Real) tor_step=(15.0 &Real) resize_vol_every=(&Size)
                  temp=(160.0 &Real) pressure=(1.0 &Real) correct_LJtruncation=(false &bool)
                  report_scorefile=(&string) dump_every=(0 &Size) report_every=(0 &Size) report_thermodynamics=(0 &Size)            
                  initial_density=(1.0 &Real) istart=(0 &Size) />

scorefxn - weights file for the simulation.
nmol_side - number of molecules per each dimension; total molecules = nmol_side^3
steps_equilibrate - number of MC steps for equilibration
steps_sim - number of MC steps for production simulation
vol_step - maximum magnitude of the total volume change movement of simulation box. Proper value may vary on nmol_side.
rot_step - maximum magnitude of the rotational movement.
tor_step - maximum magnitude of the torsion movement. Will try to rotate the torsions given in the residue file.
resize_vol_every - how often volume movement is called during MC. otherwise will randomly call either rotation or torsion movement.
temp - temperature in Kelvin
pressure - Pressure in atm.
correct_LJtruncation - whether to add the correction coming from long-range LJ interaction (by integrating over the distance from fa_max_dis to infinity); should be turned on for liquid simulation.
report_scorefile - name of the file to report energy components along the trajectory.
dump_every - how often will dump the silent file (if requested)
report_every - how often will dump the energy components to score file.
report_thermodynamics - how often will report thermodynamic properties -- currently not very useful.
initial_density - initial density of small molecules in g/cm^3. initial guess is 1.0 from water, but in general other small molecules have lower densities.
istart - simulation step to begin with; used for continuing simulation.

Restarting simulation

TBA

Liquid simulation related

All the example weights, options in xml, command line is provided in Park et al (2016).
Analyzing the result: One can calculate liquid properties such as "heat of vaporization", "density", "heat capacity", and so on, by processing the report_scorefile. For an example analysis script, please contact to Hahnbeom Park (hahnbeom@gmail.com).