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tsoc
openmm
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a61fd9a9
Commit
a61fd9a9
authored
Feb 02, 2016
by
Jason Swails
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wrappers/python/simtk/openmm/mtsintegrator.py
wrappers/python/simtk/openmm/mtsintegrator.py
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wrappers/python/simtk/openmm/mtsintegrator.py
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a61fd9a9
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@@ -45,11 +45,9 @@ class MTSIntegrator(CustomIntegrator):
...
@@ -45,11 +45,9 @@ class MTSIntegrator(CustomIntegrator):
setForceGroup() on them) that should be evaluated at different frequencies. When
setForceGroup() on them) that should be evaluated at different frequencies. When
you create the integrator, you provide a tuple for each group specifying the index
you create the integrator, you provide a tuple for each group specifying the index
of the force group and the frequency (as a fraction of the outermost time step) at
of the force group and the frequency (as a fraction of the outermost time step) at
which to evaluate it. For example:
which to evaluate it. For example:
:
```
integrator = MTSIntegrator(4*femtoseconds, [(0,1), (1,2), (2,8)])
integrator = MTSIntegrator(4*femtoseconds, [(0,1), (1,2), (2,8)])
```
This specifies that the outermost time step is 4 fs, so each step of the integrator
This specifies that the outermost time step is 4 fs, so each step of the integrator
will advance time by that much. It also says that force group 0 should be evaluated
will advance time by that much. It also says that force group 0 should be evaluated
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@@ -60,13 +58,11 @@ class MTSIntegrator(CustomIntegrator):
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@@ -60,13 +58,11 @@ class MTSIntegrator(CustomIntegrator):
less often than the bonded and direct space nonbonded interactions. The following
less often than the bonded and direct space nonbonded interactions. The following
example looks up the NonbondedForce, sets the reciprocal space interactions to their
example looks up the NonbondedForce, sets the reciprocal space interactions to their
own force group, and then creates an integrator that evaluates them once every 4 fs,
own force group, and then creates an integrator that evaluates them once every 4 fs,
but all other interactions every 2 fs
.
but all other interactions every 2 fs
::
```
nonbonded = [f for f in system.getForces() if isinstance(f, NonbondedForce)][0]
nonbonded = [f for f in system.getForces() if isinstance(f, NonbondedForce)][0]
nonbonded.setReciprocalSpaceForceGroup(1)
nonbonded.setReciprocalSpaceForceGroup(1)
integrator = MTSIntegrator(4*femtoseconds, [(1,1), (0,2)])
integrator = MTSIntegrator(4*femtoseconds, [(1,1), (0,2)])
```
For details, see Tuckerman et al., J. Chem. Phys. 97(3) pp. 1990-2001 (1992).
For details, see Tuckerman et al., J. Chem. Phys. 97(3) pp. 1990-2001 (1992).
"""
"""
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