def __init__(self):
super().__init__()
self._cmdObject('acemd',
':class:`MDEngine <htmd.apps.app.App>` object',
'MD engine', None, Acemd)
self._cmdValue(
'numsteps', 'int',
'Number of steps to run the simulations in units of 4fs', 0,
TYPE_INT, RANGE_0POS)
self._cmdValue('temperature', 'float',
'Temperature of the thermostat in Kelvin', 300,
TYPE_FLOAT, RANGE_ANY)
self._cmdValue(
'k', 'float',
'Force constant of the flatbottom potential in kcal/mol/A^2. E.g. 5',
0, TYPE_FLOAT, RANGE_ANY)
self._cmdString(
'reference', 'str',
'Reference selection to use as dynamic center of the flatbottom box.',
'none')
self._cmdString(
'selection', 'str',
'Selection of atoms to apply the flatbottom potential', 'none')
self._cmdList(
'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])
self.acemd = Acemd()
#self.acemd.binindex='input.idx'
self.acemd.extendedsystem = 'input.xsc'
self.acemd.coordinates = None
self.acemd.structure = None
self.acemd.parameters = None
self.acemd.temperature = '300'
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 = '300'
self.acemd.langevindamping = '0.1'
self.acemd.pme = 'on'
self.acemd.pmegridspacing = '1.0'
self.acemd.fullelectfrequency = '2'
self.acemd.energyfreq = '5000'
self.acemd.run = '$numsteps'
self._TCL = '''
def __init__(self):
super().__init__()
self._cmdObject('acemd',
':class:`MDEngine <htmd.apps.app.App>` object',
'MD engine', None, Acemd)
self._cmdValue('runtime', 'float', 'Running time of the simulation.',
25000, TYPE_FLOAT, RANGE_0POS)
self._cmdString(
'timeunits', 'str',
'Units for time arguments. Can be \'steps\', \'ns\' etc.', 'steps')
self._cmdValue('temperature', 'float',
'Temperature of the thermostat in Kelvin', 300,
TYPE_FLOAT, RANGE_ANY)
self._cmdValue(
'fb_k', 'float',
'Force constant of the flatbottom potential in kcal/mol/A^2. E.g. 5',
0, TYPE_FLOAT, RANGE_ANY)
self._cmdString(
'fb_reference', 'str',
'Reference selection to use as dynamic center of the flatbottom box.',
'none')
self._cmdString(
'fb_selection', 'str',
'Selection of atoms to apply the flatbottom potential', 'none')
self._cmdList(
'fb_box', 'list',
'Position of the flatbottom box in term of the reference center given as '
'[xmin, xmax, ymin, ymax, zmin, zmax]', [0, 0, 0, 0, 0, 0])
self._cmdBoolean(
'useconstantratio', 'bool',
'For membrane protein simulations set it to true so that the '
'barostat does not modify the xy aspect ratio.', False)
self._cmdDict(
'constraints', 'dict',
'A dictionary of atomselections and values of the constraint to be '
'applied (in kcal/mol/A^2). Atomselects must be mutually exclusive.',
{
'protein and noh and not name CA': 0.1,
'protein and name CA': 1
})
self._cmdValue(
'nvtsteps', 'int',
'Number of initial steps to apply NVT in units of 4fs.', 500,
TYPE_INT, RANGE_ANY)
self._cmdValue(
'constraintsteps', 'int',
'Number of initial steps to apply constraints in units of 4fs. '
'Defaults to half the simulation time.', None, TYPE_INT, RANGE_ANY)
self.acemd = Acemd()
self.acemd.coordinates = None
self.acemd.structure = None
self.acemd.parameters = None
self.acemd.temperature = '$temperature'
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 = '$temperature'
self.acemd.langevindamping = '1'
self.acemd.pme = 'on'
self.acemd.pmegridspacing = '1.0'
self.acemd.fullelectfrequency = '2'
self.acemd.energyfreq = '1000'
self.acemd.constraints = 'on'
self.acemd.consref = None
self.acemd.constraintscaling = '1.0'
self.acemd.berendsenpressure = 'on'
self.acemd.berendsenpressuretarget = '1.01325'
self.acemd.berendsenpressurerelaxationtime = '800'
self.acemd.tclforces = 'on'
self.acemd.minimize = '500'
self.acemd.run = '$numsteps'
self.acemd.TCL = ('''
set numsteps {NUMSTEPS}
set temperature {TEMPERATURE}
set nvtsteps {NVTSTEPS}
set constraintsteps {CONSTRAINTSTEPS}
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 $fb_selindex]
}
proc calcforces {} {
global ref sel numsteps fb_K fb_box nvtsteps constraintsteps
loadcoords coords
##FLATBOTTOM
if {$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]
}
##EQUIL
set step [ getstep ]
if { $step > $nvtsteps } {
berendsenpressure on
} else {
berendsenpressure off
}
if { $step > $constraintsteps } {
constraintscaling 0
} else {
constraintscaling [expr 1 - 0.95*$step/$constraintsteps]
}
}
proc calcforces_endstep { } { }
''')
def __init__(self):
super().__init__()
self._cmdObject('acemd',
':class:`MDEngine <htmd.apps.app.App>` object',
'MD engine', None, Acemd)
self._cmdValue('runtime', 'float', 'Running time of the simulation.',
0, TYPE_FLOAT, RANGE_0POS)
self._cmdString('timeunits', 'str',
'Units for runtime. Can be \'steps\', \'ns\' etc.',
'steps')
self._cmdValue('temperature', 'float',
'Temperature of the thermostat in Kelvin', 300,
TYPE_FLOAT, RANGE_ANY)
self._cmdValue(
'fb_k', 'float',
'Force constant of the flatbottom potential in kcal/mol/A^2. E.g. 5',
0, TYPE_FLOAT, RANGE_ANY)
self._cmdString(
'fb_reference', 'str',
'Reference selection to use as dynamic center of the flatbottom box.',
'none')
self._cmdString(
'fb_selection', 'str',
'Selection of atoms to apply the flatbottom potential', 'none')
self._cmdList(
'fb_box', 'list',
'Position of the flatbottom box in term of the reference center given as [xmin, xmax, ymin, ymax, zmin, zmax]',
[0, 0, 0, 0, 0, 0])
self.acemd = Acemd()
#self.acemd.binindex='input.idx'
self.acemd.extendedsystem = 'input.xsc'
self.acemd.coordinates = None
self.acemd.structure = None
self.acemd.parameters = None
self.acemd.temperature = '300'
self.acemd.restart = 'on'
self.acemd.restartfreq = '5000'
self.acemd.outputname = 'output'
self.acemd.xtcfile = 'output.xtc'
self.acemd.xtcfreq = '25000'
self.acemd.timestep = '4'
self.acemd.rigidbonds = 'all'
self.acemd.hydrogenscale = '4'
self.acemd.switching = 'on'
self.acemd.switchdist = '7.5'
self.acemd.cutoff = '9'
self.acemd.exclude = 'scaled1-4'
self.acemd.scaling14 = '1.0'
self.acemd.langevin = 'on'
self.acemd.langevintemp = '300'
self.acemd.langevindamping = '0.1'
self.acemd.pme = 'on'
self.acemd.pmegridspacing = '1.0'
self.acemd.fullelectfrequency = '2'
self.acemd.energyfreq = '5000'
self.acemd.run = '$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 $fz]
}
}
proc calcforces_endstep { } { }
''')
def __init__(self):
super().__init__()
self._cmdObject('acemd',
':class:`MDEngine <htmd.apps.app.App>` object',
'MD engine', None, Acemd)
self._cmdValue(
'numsteps', 'int',
'Number of steps to run the simulations in units of 4fs', 0,
TYPE_INT, RANGE_0POS)
self._cmdValue('temperature', 'float',
'Temperature of the thermostat in Kelvin', 300,
TYPE_FLOAT, RANGE_ANY)
self._cmdValue(
'k', 'float',
'Force constant of the flatbottom potential in kcal/mol/A^2. E.g. 5',
0, TYPE_FLOAT, RANGE_ANY)
self._cmdString(
'reference', 'str',
'Reference selection to use as dynamic center of the flatbottom box.',
'none')
self._cmdString(
'selection', 'str',
'Selection of atoms to apply the flatbottom potential', 'none')
self._cmdList(
'box', 'list',
'Position of the flatbottom box in term of the reference center given as [xmin, xmax, ymin, ymax, zmin, zmax]',
[0, 0, 0, 0, 0, 0])
self._cmdBoolean(
'useconstantratio', 'bool',
'For membrane protein simulations set it to true so that the barostat does not modify the xy aspect ratio.',
False)
self._cmdDict(
'constraints', 'dict',
'A dictionary containing as keys the atomselections of the constraints '
'and as values the constraint scaling factor. 0 factor means no constraint'
', 1 full constraints and in between values are used for scaling.'
' The order with which the constraints are applied is random, so make '
'atomselects mutually exclusive to be sure you get the correct constraints.',
{
'protein and noh and not name CA': 0.1,
'protein and name CA': 1
})
self.acemd = Acemd()
self.acemd.coordinates = None
self.acemd.structure = None
self.acemd.parameters = None
self.acemd.temperature = '$temperature'
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 = '$temperature'
self.acemd.langevindamping = '1'
self.acemd.pme = 'on'
self.acemd.pmegridspacing = '1.0'
self.acemd.fullelectfrequency = '2'
self.acemd.energyfreq = '1000'
self.acemd.constraints = 'on'
self.acemd.consref = None
self.acemd.constraintscaling = '1.0'
self.acemd.berendsenpressure = 'on'
self.acemd.berendsenpressuretarget = '1.01325'
self.acemd.berendsenpressurerelaxationtime = '800'
self.acemd.tclforces = 'on'
self.acemd.minimize = '500'
self.acemd.run = '$numsteps'
self.acemd.TCL = '''
