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tsoc
openmm
Commits
1878512f
Commit
1878512f
authored
Feb 17, 2012
by
Peter Eastman
Browse files
Modeller supports SPC/E water
parent
4412050a
Changes
2
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2693 additions
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3 deletions
+2693
-3
wrappers/python/simtk/openmm/app/data/spce.pdb
wrappers/python/simtk/openmm/app/data/spce.pdb
+2688
-0
wrappers/python/simtk/openmm/app/modeller.py
wrappers/python/simtk/openmm/app/modeller.py
+5
-3
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wrappers/python/simtk/openmm/app/data/spce.pdb
0 → 100644
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1878512f
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wrappers/python/simtk/openmm/app/modeller.py
View file @
1878512f
...
...
@@ -74,9 +74,9 @@ class Modeller(object):
"""Convert all water molecules to a different water model.
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
elif
model
==
'tip4pew'
:
sites
=
4
...
...
@@ -153,7 +153,7 @@ class Modeller(object):
Parameters:
- 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
- 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+'
...
...
@@ -192,6 +192,8 @@ class Modeller(object):
vdwRadiusPerSigma
=
0.5612310241546864907
if
model
==
'tip3p'
:
waterRadius
=
0.31507524065751241
*
vdwRadiusPerSigma
elif
model
==
'spce'
:
waterRadius
=
0.31657195050398818
*
vdwRadiusPerSigma
elif
model
==
'tip4pew'
:
waterRadius
=
0.315365
*
vdwRadiusPerSigma
elif
model
==
'tip5p'
:
...
...
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