custom SHAKE constraints, gromacs topology

[Daniel Konstantinovsky]

Hi OpenMM,

I am trying to use a gromacs-made topology to run simulations in openmm to take advantage of the faster CUDA code. My system consists of a protein, water/ions, urea, and TMAO. I need the TMAO and urea to be completely constrained bond-wise, the protein to be constrained only in the h-containing bonds, and the water to be rigid as usual. The custom constraints are in my gromacs topology in a [ constraints ] section, but I noticed that the GromacsTopFile object lacks a field for constraints, and I worry that these constraints are not being read. Is there a way to implement this combination of SHAKE constraints in OpenMM? I really want to use OpenMM because it is considerably faster than GROMACS's GPU implementation in my experience...

Thank you!
Dan


For your reference, vars(GromacsTopFile object) gives
_includeDirs
_defines
_genpairs
_currentCategory
_ifStack
_elseStack
_moleculeTypes
_molecules
_currentMoleculeType
_atomTypes
_bondTypes
_angleTypes
_dihedralTypes
_implicitTypes
_pairTypes
_cmapTypes
_nonbondTypes
_defaults
topology