Giacomo Fiorin

icon indicating a website link https://research.ninds.nih.gov/staff-directory/giacomo-fiorin-phd

icon company NIH icon location Bethesda, MD icon location Staff scientist at NIH, studying biological membranes using computational tools

Results 101 comments of Giacomo Fiorin

Cannot create object with empty config block on single line

@HanatoK You are right in principle, but are also implicitly pointing out in your comment the drawback of an external parser: people's preferences will differ substantially. This is not anyone's...

Make corrFunc and runAve restartable biases

Note: the existing `run_ave` command (5752af7, currently still undocumented) should be discontinued.

Make corrFunc and runAve restartable biases

TODO: modify the Dashboard template `colvar_with_analysis.in` accordingly.

Move cvm::atom member data to synchronized vectors within cvm::atom_group

Yeah, but then the cvc objects have to deal with changes in frame of reference, fit gradients, and such. With no solution giving a perfect division of labor, I prefer...

Move cvm::atom member data to synchronized vectors within cvm::atom_group

The atom group can easily store pointers to the arrays of gradients, and set a pointers to NULL when the corresponding CVC are deleted. To store atomic data (positions vs...

Move cvm::atom member data to synchronized vectors within cvm::atom_group

@HanatoK Whichever way you look at it, gradients and fit gradients are specific to the combination of CVC and atom group, so storage for those will be shared by both,...

Move cvm::atom member data to synchronized vectors within cvm::atom_group

I think it's more than that. With distanceVec or distanceZ it's not just the fitting part (which isn't even there all the time) but the entire function that is computed...

Move cvm::atom member data to synchronized vectors within cvm::atom_group

I can't think of a way that an architecture change, no matter how limited, *wouldn't* be involved at some point. We're discussing redundancies between different groups of the same CVC,...

Discuss Jacobian term in the doc

I'm thinking about a third option, i.e. a very brief intro section at the beginning of the chapter on biases, mentioning TI and other estimators (and the methods that use...

Smaller variant of multicol files for 3D grids (and beyond)

A semi-standard format for a 3D image is OpenDX itself (or at least the subset that is used by APBS, VMD, NAMD, Pymol, etc.). Like "multicol" it contains a header...