Comments (2)
I think I have now fixed this by ensuring that no atoms in the atomtypes
section of the GROMACS topology file are flagged as dummy atoms if the molecule is perturbable. Previously the parser would label an atom as a dummy if the Lennard-Jones term was zero. I assume that GROMACS deals with creating dummy atoms internally when running a free energy simulation, so there is no need to set this in the topology file. (The manual doesn't mention anything about dummies, or modifying the mass of the lambda = 0 or 1 state.)
I'm not sure how things work in SOMD, which uses AMBER topology files. The pert file only specifies the initial and final values of the charge and LJ values. I assume you write the topology file at lambda = 0, although I'm not sure what the mass should be for atoms that aren't present at lambda = 0.
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For reference, the Sire commit can be found here.
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