def __init__(self, _version=_config["acemdversion"]):
if _version == 2:
raise RuntimeError("Equilibration v3 only supports _version=3")
super().__init__()
self._arg(
"acemd",
":class:`Acemd <htmd.mdengine.acemd.acemd.Acemd>` object",
"Acemd class object",
None,
val.Object([Acemd2, Acemd]),
)
self._arg(
"runtime",
"float",
"Running time of the simulation.",
25000,
val.Number(float, "0POS"),
)
self._arg(
"timeunits",
"str",
"Units for time arguments. Can be 'steps', 'ns' etc.",
"steps",
val.String(),
)
self._arg(
"temperature",
"float",
"Temperature of the thermostat in Kelvin",
300,
val.Number(float, "ANY"),
)
self._arg(
"useconstantratio",
"bool",
"For membrane protein simulations set it to true so that the barostat "
"does not modify the xy aspect ratio.",
False,
val.Boolean(),
)
self._arg(
"restraintsteps",
"int",
"Number of initial steps to apply restraints in units of 4fs. Defaults "
"to half the simulation time.",
None,
val.Number(int, "ANY"),
)
self._arg(
"restraints",
"list",
"A list of restraint objects. If None will apply defaultEquilRestraints decaying over half the runtime. If no restraints are required set to empty list []."
"See :class:`AtomRestraint <htmd.mdengine.acemd.acemd.AtomRestraint>` and"
":class:`GroupRestraint <htmd.mdengine.acemd.acemd.GroupRestraint>`)",
None,
val.Object(_Restraint),
nargs="*",
)
self.acemd = Acemd()
self.acemd.coordinates = None
self.acemd.structure = None
self.acemd.parameters = None
self.acemd.restart = "on"
self.acemd.trajectoryfile = "output.xtc"
self.acemd.trajectoryperiod = 25000
self.acemd.timestep = 4
self.acemd.switching = "on"
self.acemd.switchdistance = 7.5
self.acemd.cutoff = 9
self.acemd.thermostat = "on"
self.acemd.thermostatdamping = 1
self.acemd.pme = "on"
self.acemd.barostat = "on"
self.acemd.barostatpressure = 1.01325
self.acemd.minimize = 500
def __init__(self, _version=2):
super().__init__()
self._version = _version
self._arg(
'acemd',
':class:`Acemd2 <htmd.apps.acemd.Acemd>` or :class:`Acemd <htmd.mdengine.acemd.acemd.Acemd>`'
' object', 'Acemd class object', None, val.Object([Acemd2, Acemd]))
self._arg('runtime', 'float', 'Running time of the simulation.', 25000,
val.Number(float, '0POS'))
self._arg('timeunits', 'str',
'Units for runtime. Can be \'steps\', \'ns\' etc.', 'steps',
val.String())
self._arg('temperature', 'float',
'Temperature of the thermostat in Kelvin', 300,
val.Number(float, 'ANY'))
self._arg(
'fb_k', 'float',
'Force constant of the flatbottom potential in kcal/mol/A^2. E.g. 5',
0, val.Number(float, 'ANY'))
self._arg(
'fb_reference', 'str',
'Reference selection to use as dynamic center of the flatbottom box.',
'none', val.String())
self._arg('fb_selection', 'str',
'Selection of atoms to apply the flatbottom potential',
'none', val.String())
self._arg(
'fb_box',
'list',
'Position of the flatbottom box in term of the reference center given as '
'[xmin, xmax, ymin, ymax, zmin, zmax]', [0, 0, 0, 0, 0, 0],
val.Number(float, 'ANY'),
nargs=6)
self._arg(
'useconstantratio', 'bool',
'For membrane protein simulations set it to true so that the barostat '
'does not modify the xy aspect ratio.', False, val.Boolean())
self._arg(
'useconstraints', 'bool',
'Apply constraints to the production simulation, defined by the '
'constraints parameter', False, val.Boolean())
self._arg(
'constraints', 'dict',
'A dictionary of atomselections and values of the constraint to be '
'applied (in kcal/mol/A^2). Atomselects must be mutually exclusive.',
{}, val.Dictionary(key_type=str))
self._arg(
'adaptive', 'bool',
'Set to True if making production runs for adaptive sampling.',
False, val.Boolean())
self._arg(
'restraints',
'list',
'A list of restraint objects. Only works with {}(_version=3),'
'see :class:`AtomRestraint <htmd.mdengine.acemd.acemd.AtomRestraint>` and'
':class:`GroupRestraint <htmd.mdengine.acemd.acemd.GroupRestraint>`'
')'.format(self.__class__.__name__),
None,
val.Object(_Restraint),
nargs='*')
if self._version == 2:
self.acemd = Acemd2()
self.acemd.binindex = None
self.acemd.binvelocities = None
self.acemd.bincoordinates = 'output.coor'
self.acemd.extendedsystem = 'output.xsc'
self.acemd.coordinates = None
self.acemd.structure = None
self.acemd.parameters = None
self.acemd.temperature = None
self.acemd.restart = 'on'
self.acemd.restartfreq = '5000'
self.acemd.outputname = 'output'
self.acemd.xtcfile = 'output.xtc'
self.acemd.xtcfreq = '25000'
self.acemd.timestep = '4'
self.acemd.rigidbonds = 'all'
self.acemd.hydrogenscale = '4'
self.acemd.switching = 'on'
self.acemd.switchdist = '7.5'
self.acemd.cutoff = '9'
self.acemd.exclude = 'scaled1-4'
self.acemd.scaling14 = '1.0'
self.acemd.langevin = 'on'
self.acemd.langevintemp = None
self.acemd.langevindamping = '0.1'
self.acemd.pme = 'on'
self.acemd.pmegridspacing = '1.0'
self.acemd.fullelectfrequency = '2'
self.acemd.energyfreq = '5000'
self.acemd.consref = None
self.acemd.run = '$numsteps'
self.acemd.TCL = ('''
set numsteps {NUMSTEPS}
set fb_refindex {{ {REFINDEX} }}
set fb_selindex {{ {SELINDEX} }}
set fb_box {{ {BOX} }}
set fb_K {KCONST}
#
''', '''
proc flatbot1d {x xm xM fb_K} {
set f 0
if {$x < $xm} {
set f [expr $fb_K*[expr $xm-$x]]
}
if {$x > $xM} {
set f [expr $fb_K*[expr $xM-$x]]
}
return $f
}
proc calcforces_init {} {
global ref sel fb_refindex fb_selindex
berendsenpressure off
set ref [addgroup $fb_refindex]
set sel [addgroup $fb_selindex]
}
proc calcforces {} {
global ref sel fb_K fb_box
loadcoords coords
##FLATBOTTOM
if {$fb_K>0} {
set r0 $coords($ref)
set r1 $coords($sel)
set dr [vecsub $r1 $r0]
set fx [flatbot1d [lindex $dr 0] [lindex $fb_box 0] [lindex $fb_box 1] $fb_K]
set fy [flatbot1d [lindex $dr 1] [lindex $fb_box 2] [lindex $fb_box 3] $fb_K]
set fz [flatbot1d [lindex $dr 2] [lindex $fb_box 4] [lindex $fb_box 5] $fb_K]
#print "dr: $dr fx: $fx fy: $fy fz: $fz"
addforce $sel [list $fx $fy $fz]
}
}
proc calcforces_endstep { } { }
''')
elif self._version == 3:
self.acemd = Acemd()
self.acemd.binvelocities = None
self.acemd.bincoordinates = 'output.coor'
self.acemd.extendedsystem = 'output.xsc'
self.acemd.coordinates = None
self.acemd.structure = None
self.acemd.parameters = None
self.acemd.restart = 'on'
self.acemd.trajectoryfile = 'output.xtc'
self.acemd.trajectoryfreq = 25000
self.acemd.timestep = 4
self.acemd.switching = 'on'
self.acemd.switchdist = 7.5
self.acemd.cutoff = 9
self.acemd.thermostat = 'on'
self.acemd.thermostatdamping = 0.1
self.acemd.pme = 'on'
else:
raise ValueError(
'_version can not be {}. Choose either 2 or 3.'.format(
self._version))
def __init__(self):
super().__init__()
self._arg(
"acemd",
":class:`Acemd <htmd.mdengine.acemd.acemd.Acemd>`"
" object",
"Acemd class object",
None,
val.Object(Acemd),
)
self._arg(
"runtime",
"float",
"Running time of the simulation.",
25000,
val.Number(float, "0POS"),
)
self._arg(
"timeunits",
"str",
"Units for runtime. Can be 'steps', 'ns' etc.",
"steps",
val.String(),
)
self._arg(
"temperature",
"float",
"Temperature of the thermostat in Kelvin",
300,
val.Number(float, "ANY"),
)
self._arg(
"fb_k",
"float",
"Force constant of the flatbottom potential in kcal/mol/A^2. E.g. 5",
0,
val.Number(float, "ANY"),
)
self._arg(
"fb_reference",
"str",
"Reference selection to use as dynamic center of the flatbottom box.",
"none",
val.String(),
)
self._arg(
"fb_selection",
"str",
"Selection of atoms to apply the flatbottom potential",
"none",
val.String(),
)
self._arg(
"fb_box",
"list",
"Position of the flatbottom box in term of the reference center given as "
"[xmin, xmax, ymin, ymax, zmin, zmax]",
[0, 0, 0, 0, 0, 0],
val.Number(float, "ANY"),
nargs=6,
)
self._arg(
"useconstantratio",
"bool",
"For membrane protein simulations set it to true so that the barostat "
"does not modify the xy aspect ratio.",
False,
val.Boolean(),
)
self._arg(
"useconstraints",
"bool",
"Apply constraints to the production simulation, defined by the "
"constraints parameter",
False,
val.Boolean(),
)
self._arg(
"constraints",
"dict",
"A dictionary of atomselections and values of the constraint to be "
"applied (in kcal/mol/A^2). Atomselects must be mutually exclusive.",
{},
val.Dictionary(key_type=str),
)
self._arg(
"adaptive",
"bool",
"Set to True if making production runs for adaptive sampling.",
False,
val.Boolean(),
)
self._arg(
"restraints",
"list",
"A list of restraint objects."
"See :class:`AtomRestraint <htmd.mdengine.acemd.acemd.AtomRestraint>` and"
":class:`GroupRestraint <htmd.mdengine.acemd.acemd.GroupRestraint>`"
")",
None,
val.Object(_Restraint),
nargs="*",
)
self.acemd = Acemd()
self.acemd.binvelocities = None
self.acemd.bincoordinates = "output.coor"
self.acemd.extendedsystem = "output.xsc"
self.acemd.coordinates = None
self.acemd.structure = None
self.acemd.parameters = None
self.acemd.restart = "on"
self.acemd.trajectoryfile = "output.xtc"
self.acemd.trajectoryperiod = 25000
self.acemd.timestep = 4
self.acemd.switching = "on"
self.acemd.switchdistance = 7.5
self.acemd.cutoff = 9
self.acemd.thermostat = "on"
self.acemd.thermostatdamping = 0.1
self.acemd.pme = "on"