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tsoc
openmm
Commits
05dd85de
Commit
05dd85de
authored
May 04, 2015
by
peastman
Browse files
Updated documentation for addSolvent()
parent
92dfd1ff
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docs-source/usersguide/application.rst
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docs-source/usersguide/application.rst
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05dd85de
...
...
@@ -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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