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tsoc
openmm
Commits
38f286e5
Commit
38f286e5
authored
Dec 22, 2013
by
Jason Swails
Browse files
Unit-ify the 0 in implicitSolventKappa.
parent
3ca3fe54
Changes
2
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2 changed files
with
8 additions
and
5 deletions
+8
-5
wrappers/python/simtk/openmm/app/amberprmtopfile.py
wrappers/python/simtk/openmm/app/amberprmtopfile.py
+3
-2
wrappers/python/simtk/openmm/app/internal/amber_file_parser.py
...ers/python/simtk/openmm/app/internal/amber_file_parser.py
+5
-3
No files found.
wrappers/python/simtk/openmm/app/amberprmtopfile.py
View file @
38f286e5
...
...
@@ -142,7 +142,8 @@ class AmberPrmtopFile(object):
def
createSystem
(
self
,
nonbondedMethod
=
ff
.
NoCutoff
,
nonbondedCutoff
=
1.0
*
unit
.
nanometer
,
constraints
=
None
,
rigidWater
=
True
,
implicitSolvent
=
None
,
implicitSolventKappa
=
0.0
,
soluteDielectric
=
1.0
,
solventDielectric
=
78.5
,
implicitSolventKappa
=
0.0
*
(
1
/
unit
.
nanometer
),
soluteDielectric
=
1.0
,
solventDielectric
=
78.5
,
removeCMMotion
=
True
,
hydrogenMass
=
None
,
ewaldErrorTolerance
=
0.0005
):
"""Construct an OpenMM System representing the topology described by this prmtop file.
...
...
@@ -154,7 +155,7 @@ class AmberPrmtopFile(object):
Allowed values are None, HBonds, AllBonds, or HAngles.
- rigidWater (boolean=True) If true, water molecules will be fully rigid regardless of the value passed for the constraints argument
- implicitSolvent (object=None) If not None, the implicit solvent model to use. Allowed values are HCT, OBC1, OBC2, GBn, or GBn2.
- implicitSolventKappa (float=0.0) The Debye-screening parameter corresponding to ionic strength used for implicit solvent
- implicitSolventKappa (float=0.0
*1/unit.nanometer
) The Debye-screening parameter corresponding to ionic strength used for implicit solvent
- soluteDielectric (float=1.0) The solute dielectric constant to use in the implicit solvent model.
- solventDielectric (float=78.5) The solvent dielectric constant to use in the implicit solvent model.
- removeCMMotion (boolean=True) If true, a CMMotionRemover will be added to the System
...
...
wrappers/python/simtk/openmm/app/internal/amber_file_parser.py
View file @
38f286e5
...
...
@@ -565,9 +565,11 @@ class PrmtopLoader(object):
# AMBER System builder (based on, but not identical to, systemManager from 'zander')
#=============================================================================================
def
readAmberSystem
(
prmtop_filename
=
None
,
prmtop_loader
=
None
,
shake
=
None
,
gbmodel
=
None
,
soluteDielectric
=
1.0
,
solventDielectric
=
78.5
,
implicitSolventKappa
=
0.0
,
nonbondedCutoff
=
None
,
nonbondedMethod
=
'NoCutoff'
,
scee
=
None
,
scnb
=
None
,
mm
=
None
,
verbose
=
False
,
EwaldErrorTolerance
=
None
,
flexibleConstraints
=
True
,
rigidWater
=
True
,
elements
=
None
):
def
readAmberSystem
(
prmtop_filename
=
None
,
prmtop_loader
=
None
,
shake
=
None
,
gbmodel
=
None
,
soluteDielectric
=
1.0
,
solventDielectric
=
78.5
,
implicitSolventKappa
=
0.0
*
(
1
/
units
.
nanometer
),
nonbondedCutoff
=
None
,
nonbondedMethod
=
'NoCutoff'
,
scee
=
None
,
scnb
=
None
,
mm
=
None
,
verbose
=
False
,
EwaldErrorTolerance
=
None
,
flexibleConstraints
=
True
,
rigidWater
=
True
,
elements
=
None
):
"""
Create an OpenMM System from an Amber prmtop file.
...
...
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