The CONTROL File Directives

The directives available are as follows.

		 directive: 		 meaning: 

  		 

all pairs 		 use all pairs for electrostatic calculations

cap f		 cap forces during equilibration period

f is maximum cap in units of kT/Å

(default f=1000)

close time f 		 set job closure time to fseconds

collect 		 include equilibration data in overall statistics 

coul 		 calculate coulombic forces 

cut  f 		 set required forces cutoff to f (Å)

distan 		 calculate coulombic forces using distance dependentdielectric

delr f 		 set Verlet neighbour list shell width to f (Å) 

ensemble nve 		 select NVE ensemble (default) 

ensemble nvt ber f 


select NVT ensemble with Berendsen thermostat


with relaxation constant f (ps) 

ensemble nvt evans 


select NVT ensemble with Evans thermostat

ensemble nvt hoover f


select NVT ensemble with Hoover-Nose thermostat


with relaxation constant f (ps) 

ensemble npt ber $f_{1}~f_{2}$ 


select Berendsen NPT ensemble with $f_{1},~f_{2}$ 


as the thermostat and  barostat relaxation times (ps) 

ensemble npt hoover $f_{1}~f_{2}$ 


select Hoover NPT ensemble with  $f_{1},~f_{2}$ 


as the thermostat and barostat relaxation times (ps) 

ensemble nst ber $f_{1}~f_{2}$ 


select Berendsen N$\mbox{$\underline{\underline{\bf\sigma}}$}$Tensemble, with $f_{1},~f_{2}$


as the thermostat and  barostat relaxation times (ps) 

ensemble nst hoover $f_{1}~f_{2}$ 


select Hoover N$\mbox{$\underline{\underline{\bf\sigma}}$}$T ensemble with $f_{1},~f_{2}$ 


as the thermostat and barostat relaxation times (ps) 

ensemble pmf		 select (NVE) potential of mean force ensemble 

eps f		 set relative dielectric constant to f(default 1.0)

equil n 		 equilibrate simulation for first ntimesteps

ewald precision f 		select Ewald sum for electrostatics, with  


automatic parameter optimisation ($0<f<.5$) 

ewald sum  $\alpha$ k1 k2 k3 


select Ewald sum for electrostatics, with:

$\alpha$ $=$ Ewald convergence parameter (Å$^{-1}$)

k1 $=$ maximum k-vector index in x-direction

k2 $=$ maximum k-vector index in y-direction

k3 $=$ maximum k-vector index in z-direction

finish 		 close the CONTROL file (last data record)

hke precision f i j 		select HK-Ewaldsum for electrostatics, with  


automatic parameter optimisation ($0<f<.5$) 

i $=$ required order of HKE expansion (recommend 1)

j $=$ required lattice sum order (recommend 1)

hke sum  $\alpha$ k1 k2 i j 


select HK-Ewald sum for electrostatics, with:

$\alpha$ $=$ Ewald convergence parameter (Å$^{-1}$)

k1 $=$ maximum g-vector index in x-direction

k2 $=$ maximum g-vector index in y-direction

nhko $=$ required order of HKE expansion (recommend 1)

nlatt $=$ required lattice sum order (recommend 1)

job time f		 set job time to f seconds 

mult n 		 set multiple timestep (multi-step)interval (activated when n$>$2)

no elec 		 ignore coulombic interactions

no vdw 		 ignore short range (non-bonded) interactions

pres f 		 set required system pressure to f k.bars

(target pressure for constant pressure ensembles)

prim  f		 set primary cutoff to f (Å) 

(for multiple timestep algorithm only)

print n 		 print system data every n timesteps 

print rdf 		 print radial distribution functions 

quaternion f 		 set quaternion tolerance to  f (default 10$^{-8}$)

rdf f 		 calculate radial distribution functions atintervals


of f timesteps

reaction		 select reaction field electrostatics 

restart 		 restart job from end point of previous run

(i.e. continue current simulation)

restart scale 		 restart job from previous run with temperaturescaling

(i.e. begin a new simulation from older run)

scale n 		 rescale atomic velocities every n steps(during equilibration) 

shake f 		 set shake tolerance to f  (default10$^{-8}$)

shift 		 calculate  electrostatic forces using shiftedcoulombic potential

spme precision f 		select Ewald sum for electrostatics, with  


automatic parameter optimisation ($0<f<.5$) 

spme sum  $\alpha$ k1 k2 k3 


select Ewald sum for electrostatics, with:

$\alpha$ $=$ Ewald convergence parameter (Å$^{-1}$)

k1 $=$ maximum k-vector index in x-direction

k2 $=$ maximum k-vector index in y-direction

k3 $=$ maximum k-vector index in z-direction

stack n 		 set rolling average stack to ntimesteps 

stats n 		 accumulate statistics data every ntimesteps

steps n 		 run simulation for n timesteps 

temp f 		 set required simulation temperature to f  K

traj i j k 		 write HISTORY file with controls:

i $=$ start timestep for dumping configurations

j $=$ timestep interval between  configurations

k $=$ data level (i.e. variable keytrj see table 4.3)

timestep f 		 set timestep to f ps

zden 		 calculate the z-density profile 

zero 		 perform zero temperature MD run