Comments (11)
This is the problem that @jchodera is observing with the lack of bond. Parmed does not perceive constraints, and so there is just no bond. I'm going to add the constraint stuff in the next PR.
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Discussed in here.
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Constraint tolerance is a context parameter in OpenMM, no? Is there a good way to deal with this in GeometryEngine
?
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Constraint tolerance is an integrator parameter!
http://docs.openmm.org/6.3.0/api-python/classsimtk_1_1openmm_1_1openmm_1_1Integrator.html#a311f37a6d317055063bd8b390ba47737
from perses.
Oops. Thanks! Still not accessible to GeometryEngine
as written, though. Should GeometryEngine
accept constraint tolerance as a parameter? Should it be in the constructor?
from perses.
Oops. Thanks! Still not accessible to GeometryEngine as written, though. Should GeometryEngine accept constraint tolerance as a parameter? Should it be in the constructor?
Are we talking about constraint tolerance or what kind of bond constraints to use?
We definitely want to specify what kind of bond constraints to use, but that is permitted already. See this example. Note that these are all changed to constraints=None
in my PR #109
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Constraint tolerance. GeometryEngine
can figure out whether all bonds or H bonds are constrained (but not whether there are angle constraints) in the current code. I assume that bond_length-constraint
will not always be exactly 0, and I assumed that the constraint_tolerance
would be a good tolerance.
if np.abs(bond_length-constraint)<constraint_tolerance:
logp_bond = 0.0
else:
logp_bond = -np.inf
from perses.
I'm confused. Doesn't GeometryEngine
take a System
as input? The System
allows you to enumerate which bonds are constrained via
for index in range(system.getNumConstraints()):
[atom1, atom2, r] = system.getConstraint(index)
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Yes, I know that. I can tell which bonds are constrained. The problem is comparing the constraint to the actual bond length, and determining whether that difference is within the tolerance.
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if we did something like
if np.abs(bond_length-constraint)==0.0:
logp_bond = 0.0
else:
logp_bond = -np.inf
it would probably fail every time.
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Concluded that we will assume constraints are iterated to convergence, so if there is a bond constraint, we will use a logp of 0.0.
Resolved in #113
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Related Issues (20)
- Integrate new atom mappers HOT 7
- Write initial initial and final structures in subdir
- AtomMapper fails when scaffolds have radicals HOT 1
- Creating legacy 0.10.x branch for longer term support -- main branch will become `gufe` refactor HOT 1
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- Error with spectator ligands HOT 8
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- Update README? HOT 1
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