Python_MDSetup

How can I create a molecular dynamics (MD) simulation with water molecules?

When using explicit solvent periodic boundary conditions have to be used.

NOTE: Running the following script in BALLView creates a large number of representations (water molecules) as well. To reduce runnging time set the default representation to 'Line Model' before.

{{{ #!python

create an Amber forcefield

af = AmberFF()

get the molecule

s = getSystem(0)

get the dimensions of the molecule

bbp = BoundingBoxProcessor() s.apply(bbp)

enlarge the box around the molecule by some scalar

sc = 10.

enlarge the box by the scalar factor

vl = bbp.getLower() - Vector3(sc) vu = bbp.getUpper() + Vector3(sc)

tell the forcefield about being a periodic box

af.options.setBool("periodic_box_enabled", True) af.options.setVector("periodic_box_lower", vl) af.options.setVector("periodic_box_upper", vu)

initialize the forcefield with these options

af.setup(s)

create the box containing molecule and explicit solvent

b = SimpleBox3() b.set(vl, vu)

initialize a small building block, in which the forcefield holds

p = PeriodicBoundary(af)

fill the entire box (b) with copies of p

p.setBox(b)

setup

p.setup()

for graphical representation

new_box = p.getBox()

v1 = new_box.a # get the anchor v2 = Vector3(new_box.getWidth(), 0, 0) v3 = Vector3(0, new_box.getHeight(), 0) v4 = Vector3(0, 0, new_box.getDepth())

colored_box = Box(v1, v2, v3, v4) colored_box.setColor(ColorRGBA(1, 0, 0, 0.8)) r = Representation() r.insert(colored_box)

update the representation

getMainControl().insert(r) getMainControl().update(r)

getMainControl().updateRepresentationsOf(s)

}}}