Jérôme Hénin

A related point: I've noted that in practice, fitting is nearly often done per-CVC and not per atom group. I can't think of an example where different atom groups are...

I agree that gradients and fit gradients are specific to the combination of CVC and atom group. But while an atom group could potentially be shared and re-used between different...

There are cases for distanceZ when several projections are needed, yes - that would be good to address as well. For distanceVec, I can't think of a case. Here I...

The places I can see in the doc where that could fit is either in the ABF section where the Jacobian term is already mentioned, or in the Thermodynamic integration...

Looked into it, and I found it difficult to write. Can you take a stab at it, if you have a precise idea what to say?

Here is a plan: - take the logic currently in the ABF bias and move it into: in dimension higher than 2, write a DX file in addition to multicol....

Yes, I agree that we don't want to add a DX parser in there. The state file format seems ok, but we'll need the same flexibility offered by multicol: specifically...

This is caused by a problem at the beginning of Make.depends: ``` $(CC) $(CXXFLAGS) $(COPTO)obj/AVXTiles.o $(COPTC) src/AVXTiles.c $(CC) $(CXXFLAGS) $(COPTO)obj/AVXTilesKernel.o $(COPTC) src/AVXTilesKernel.c $(CC) $(CXXFLAGS) $(COPTO)obj/AVXTileLists.o $(COPTC) src/AVXTileLists.c obj/ComputeMoa.o: \ obj/.exists...

Alternately, it could come from various conflicts between the Makefile of NAMD and a previous version. It's hard to say more without more details.

Based on my experience today, I would recommend: 1) check all Makefiles for traces of incomplete merges (lines with >) and remove them :-) 2) make clean 3) make depends...