The -s option in gmx saxs

GROMACS version: 2020.4
GROMACS modification: No
Here post your question
I am new to Gromacs. I have a trajectory file calculated from other MD code, and I would like to use Gromacs to calculate SAXS. So far I was able to convert my trajectory to .gro format. The problem is the structure file (-s option), since I am not producing my trajectory file from Gromacs itself, I don’t have the .tpr file, I am wondering if I can just put one of each type of molecule in a .gro file (or a .pdb file) and treat it as a structure file, or I should put the first frame of the whole system in a .gro file? Which one yields the correct SAXS pattern for the whole system? What is the correct way of specifying the -s option without having the .tpr file?

Shao-Chun Lee

Also, how does Gormacs recognize the atom type? For example, the O and H in WATER are often named as OW and HW1, HW2 in Gormacs. So how does Gormacs map these atom name to the actual element?

The structure in -s has to match the contents of the system and is used as a reference for masses and connectivity. A .gro file has neither. Masses will be guessed from atommass.dat but if your system has anything unusual, that may cause problems. Using .gro for a reference also prevents the program from dealing with periodicity because there is no topological information.

Thank you for your reply. But how about the atomic form factor? Does Gromacs guess the atom type based on the same way how it guesses atomic mass? Actually, I am confused about the need for topology and masses.

The form factor is based on the element itself. Without a topology, again this is guessed based on atom name. With a topology that includes mass, then the element is unambiguous. If one has an atom named CA, is that an alpha carbon in a protein or is it a calcium ion? The former is going to be matched first (first character C) but if you actually have calcium, you’ll get an incorrect result.