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tsoc
openmm
Commits
0df0cd8b
"...reference/src/SimTKReference/SimTKOpenMMUtilities.cpp" did not exist on "90f31a686e9d4d3dc6bb2e845cf9c01215932a46"
Commit
0df0cd8b
authored
Jun 11, 2009
by
Michael Sherman
Browse files
Fix some comments.
parent
acf79ffc
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examples/HelloSodiumChlorideInC.c
examples/HelloSodiumChlorideInC.c
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examples/HelloSodiumChlorideInC.c
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0df0cd8b
...
@@ -171,15 +171,16 @@ struct MyOpenMMData_s {
...
@@ -171,15 +171,16 @@ struct MyOpenMMData_s {
* INITIALIZE OpenMM DATA STRUCTURES
* INITIALIZE OpenMM DATA STRUCTURES
* --------------------------------------------------------------------------
* --------------------------------------------------------------------------
* We take these actions here:
* We take these actions here:
* (1) Allocate a MyOpenMMData structure to hang on to OpenMM data structures
* (1) Load any available OpenMM plugins, e.g. Cuda and Brook.
* (2) Allocate a MyOpenMMData structure to hang on to OpenMM data structures
* in a manner which is opaque to the caller.
* in a manner which is opaque to the caller.
* (2) Allocate the OpenMM objects which persist from call to call.
* (3) Fill the OpenMM::System with the force field parameters we want to
* (3) Fill the OpenMM::System with the force field parameters we want to
* use and the particular set of atoms to be simulated.
* use and the particular set of atoms to be simulated.
* (4) Create an Integrator and a Context associating the Integrator with
* (4) Create an Integrator and a Context associating the Integrator with
* the System.
* the System.
* (5) Select the OpenMM platform to be used.
* (5) Select the OpenMM platform to be used.
* (6) Return the MyOpenMMData struct and the name of the Platform in use.
* (6) Return an opaque pointer to the MyOpenMMData struct and the name
* of the Platform in use.
*
*
* Note that this function must understand the calling MD code's molecule and
* Note that this function must understand the calling MD code's molecule and
* force field data structures so will need to be customized for each MD code.
* force field data structures so will need to be customized for each MD code.
...
@@ -222,7 +223,7 @@ myInitializeOpenMM( const MyAtomInfo atoms[],
...
@@ -222,7 +223,7 @@ myInitializeOpenMM( const MyAtomInfo atoms[],
* (1) System needs to know the masses.
* (1) System needs to know the masses.
* (2) NonbondedForce needs charges,van der Waals properties (in MD units!).
* (2) NonbondedForce needs charges,van der Waals properties (in MD units!).
* (3) GBSA needs charge, radius, and scale factor.
* (3) GBSA needs charge, radius, and scale factor.
* (
3
) Collect default positions for initializing the simulation later. */
* (
4
) Collect default positions for initializing the simulation later. */
initialPosInNm
=
OpenMM_Vec3Array_create
(
0
);
initialPosInNm
=
OpenMM_Vec3Array_create
(
0
);
for
(
n
=
0
;
*
atoms
[
n
].
pdb
;
++
n
)
{
for
(
n
=
0
;
*
atoms
[
n
].
pdb
;
++
n
)
{
const
MyAtomInfo
*
atom
=
&
atoms
[
n
];
const
MyAtomInfo
*
atom
=
&
atoms
[
n
];
...
...
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