Hi, I’m fairly new to molecular dynamics. I wanted to ask: as the RMSF is computed relative to the averagre coordinates over the trajectory, is, in GROMACS, the least square fitting done on all the atoms of the reference structure (or just the backbone or the C-alpha)? and if the least square fitting is done only for the section selected in the index file (if one choose to calculate on just a portion of the structure)?
Thanks in advance to anyone.
https://manual.gromacs.org/current/onlinehelp/gmx-rmsf.html
lets say if you create a index of 10 residues out of 100 and you selected those group with respect to those group, you will get rmsf for that 10 residue.
Thank you for your reply, @scinikhil! sorry for my belatedness and my english, I’m not a native speaker.Iexpressed myself badly. I understand that if I create an index of0 residues out of 100 and select those group, I’ll get rmsf for that 10 residue. What I don’t understand is what happens before; To calculate the RMSF you have to calculate the least squares on a reference structure to know if the position of the atom varies. I wanted to ask if this calculcation is done on the whole structure, only the residues you choose with the index files, and, if it is calculated on all the atoms of that portion.
Thanks and sorry
it depends on the residue you choose, for example if you wanted to calculate the rmsf of backbone atoms, you need to select both reference and ‘selection’ from the backbone
Thank you for your patience explaining it to me, @scinikhil. I understood it now.