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mosdef-hub / reproducibility_study

Repo for data collection, discussion, etc for a MoSDeF reproducibility study.
MIT License
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What constraints are needed for MD simulations? #84

Closed daico007 closed 2 years ago

daico007 commented 3 years ago

I am running into some issues when using with constraints = all-angles for a box of ethanol in GROMACS (with the LINCS algorithm). The simulation ran fine with constraints = all-bonds, so I am just wondering what is the appropriate constraints we should use for the project or for MD specifically?

jennyfothergill commented 3 years ago

We are not using any bond/angle constraints in HOOMD. Does your simulation have issue without constraints?

daico007 commented 3 years ago

Our simulations are having issues with constraints (too many warnings), so I think we gonna edit to production run to remove the constraints.

jennyfothergill commented 2 years ago

I think this issue can be closed. Constraint parameters for water are documented in the project doc--although HOOMD uses a completely rigid model for water. Benzene is also rigid. Pentane has two models and one has constrained bonds. To my knowledge, no constraints are applied to ethanol.