"openmmapi/src/DPDIntegratorUtilities.cpp" did not exist on "a711ce2a1407d4f6ad80c797040d92341f94d03a"
Commit 05dd85de authored by peastman's avatar peastman
Browse files

Updated documentation for addSolvent()

parent 92dfd1ff
......@@ -1405,8 +1405,13 @@ size, you can specify one:
modeller.addSolvent(forcefield, boxSize=Vec3(5.0, 3.5, 3.5)*nanometers)
This requests a 5 nm by 3.5 nm by 3.5 nm box. Another option is to specify a
padding distance:
This requests a 5 nm by 3.5 nm by 3.5 nm box. For a non-rectangular box, you
can specify the three box vectors defining the unit cell:
::
modeller.addSolvent(forcefield, boxVectors=(avec, bvec, cvec))
Another option is to specify a padding distance:
::
modeller.addSolvent(forcefield, padding=1.0*nanometers)
......@@ -1416,6 +1421,14 @@ then creates a cubic box of width (solute size)+2*(padding). The above line
guarantees that no part of the solute comes closer than 1 nm to any edge of the
box.
Finally, you can specify the exact number of solvent molecules (including both
water and ions) to add. This is useful when you want to solvate several different
conformations of the same molecule while guaranteeing they all have the same
amount of solvent:
::
modeller.addSolvent(forcefield, numAdded=5000)
By default, :meth:`addSolvent` creates TIP3P water molecules, but it also supports other
water models:
::
......
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