lohedges
commented
6 years ago Thanks, this is good to know. It would be very easy to give the user the ability to specify how the dummy coordinates are set as a keyword option when calling the merge function. Do you know where in FESetup the coordinates are mixed so I can take a look at how its implemented.
As a related question, do you know how the various codes, e.g. Gromacs, handle the dummy atoms coordinates? That is, do they do any mixing for you, or do they just take the bare coordinates from the input file and run with those? I guess we will generally be doing some equilibration at the start of each lambda stage, so it's possible it doesn't matter too much anyway. (Apart from very strained configurations, perhaps.)
jmichel80
Documenting a difference in behaviour between the MCS BSS and FESetup implementations.
scripts/test_mapping_methane_toluene.py
generates a merged molecule wth a topology comparable to FESetup (with a local copy of findmcs.cpp modified to match hydrogens to heavy atoms). However the coordinates of the dummy atoms in merged0.pdb (the ring atoms, apart from the hydrogen/carbon atom) are those from the aligned toluene.pdb molecule. This means that the bonded geometry around the dummy/non-dummy atoms is distorted. See picture below, showing long bond lengths and low angle for the side of the benzyl ring bonded to the methyl.
By contrast here is the morph input generated by FESetuo for methane->toluene
The difference is that in FESetup the Cartesian coordinates of the dummy atoms are worked out by mixing the coordinates of the mapped atoms in topology0 (methane), and the internal coordinates of the unmapped atoms in topology1 (toluene). In this case here in effect the benzyl ring is translated towards the methyl group so the methane molecule geometry is not distorted.
More testing is needed to determine whether one implementation is better than the other. To summarise:
The BSS implementation does not update coordinates, but generates initial conformations that are potentially highly strained The FESetup implementation generates initial conformations with low intramolecular energetics, but potentially changes intermolecular energetics.