Commit 1878512f authored by Peter Eastman's avatar Peter Eastman
Browse files

Modeller supports SPC/E water

parent 4412050a
This diff is collapsed.
...@@ -74,9 +74,9 @@ class Modeller(object): ...@@ -74,9 +74,9 @@ class Modeller(object):
"""Convert all water molecules to a different water model. """Convert all water molecules to a different water model.
Parameters: Parameters:
- model (string='tip3p') the water model to convert to. Supported values are 'tip3p', 'tip4pew', and 'tip5p'. - model (string='tip3p') the water model to convert to. Supported values are 'tip3p', 'spce', 'tip4pew', and 'tip5p'.
""" """
if model == 'tip3p': if model in ('tip3p', 'spce'):
sites = 3 sites = 3
elif model == 'tip4pew': elif model == 'tip4pew':
sites = 4 sites = 4
...@@ -153,7 +153,7 @@ class Modeller(object): ...@@ -153,7 +153,7 @@ class Modeller(object):
Parameters: Parameters:
- forcefield (ForceField) the ForceField to use for determining van der Waals radii and atomic charges - forcefield (ForceField) the ForceField to use for determining van der Waals radii and atomic charges
- model (string='tip3p') the water model to use. Supported values are 'tip3p', 'tip4pew', and 'tip5p'. - model (string='tip3p') the water model to use. Supported values are 'tip3p', 'spce', 'tip4pew', and 'tip5p'.
- boxSize (Vec3=None) the size of the box to fill with water - boxSize (Vec3=None) the size of the box to fill with water
- padding (distance=None) the padding distance to use - padding (distance=None) the padding distance to use
- positiveIon (string='Na+') the type of positive ion to add. Allowed values are 'Cs+', 'K+', 'Li+', 'Na+', and 'Rb+' - positiveIon (string='Na+') the type of positive ion to add. Allowed values are 'Cs+', 'K+', 'Li+', 'Na+', and 'Rb+'
...@@ -192,6 +192,8 @@ class Modeller(object): ...@@ -192,6 +192,8 @@ class Modeller(object):
vdwRadiusPerSigma = 0.5612310241546864907 vdwRadiusPerSigma = 0.5612310241546864907
if model == 'tip3p': if model == 'tip3p':
waterRadius = 0.31507524065751241*vdwRadiusPerSigma waterRadius = 0.31507524065751241*vdwRadiusPerSigma
elif model == 'spce':
waterRadius = 0.31657195050398818*vdwRadiusPerSigma
elif model == 'tip4pew': elif model == 'tip4pew':
waterRadius = 0.315365*vdwRadiusPerSigma waterRadius = 0.315365*vdwRadiusPerSigma
elif model == 'tip5p': elif model == 'tip5p':
......
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