Sample control file

Energy minimization with positional restraints on protein heavy atoms

In the initial structure, there may be artificial atomic crash in some parts of the system, which causes unstable energy minimization. The keywords contact_check = YES and nonb_limiter = YES allow us to avoid such situation. These options can reduce large forces on the crashing atoms. For details, please see the user manual ([ENERGY] section).

[INPUT]
topfile  = top_all36_prot.rtf, top_all36_lipid.rtf  # topology file
parfile  = par_all36_prot.prm, par_all36_lipid.prm  # parameter file
strfile  = toppar_water_ions.str  # stream file
psffile  = ionized.psf            # protein structure file
pdbfile  = ionized.pdb            # initial structure
reffile  = ionized.pdb            # reference coordinates for restraints
 
[OUTPUT]
dcdfile  = min.dcd          # DCD trajectory file
rstfile  = min.rst          # restart file
 
[ENERGY]
forcefield       = CHARMM   # CHARMM force field
electrostatic    = PME      # Particle Mesh Ewald method
switchdist       = 10.0     # switch distance
cutoffdist       = 12.0     # cutoff distance
pairlistdist     = 13.5     # pair-list distance
vdw_force_switch = YES      # force switch option for van der Waals
pme_nspline      = 4        # order of B-spline in [PME]
pme_max_spacing  = 1.0      # max grid spacing 
contact_check    = YES      # check atomic crash
nonb_limiter     = YES      # failure caused by atomic crash is avoided

[MINIMIZE]
method           = SD       # Steepest descent method
nsteps           = 5000     # number of minimization steps
eneout_period    =  100     # energy output period
crdout_period    =  100     # coordinates output period
rstout_period    = 5000     # restart output period
nbupdate_period  =   10     # nonbond update period
 
[BOUNDARY]
type             = PBC      # periodic boundary condition
box_size_x       = 128.000  # box size (x) in [PBC]
box_size_y       = 128.000  # box size (y) in [PBC]
box_size_z       = 144.000  # box size (z) in [PBC]

[SELECTION]
group1           = sid:PROA and heavy
 
[RESTRAINTS]
nfunctions       = 1        # number of functions
function1        = POSI     # restraint function type
direction1       = ALL      # direction
constant1        = 1.0      # force constant
select_index1    = 1        # restrained groups