About the msd command in gromacs

User discussions
1

GROMACS version:2023
GROMACS modification: No
In the simulation, if the MSD of the water molecules surrounding the S atom is required, how should I write the command? The command I used is gmx -f md.xtc -s md.tpr -o msd.xvg, but I can only find the msd of the overall water molecules in the system.

2

for this you first make an index file to include all the indexes of that ‘S’ atom using make_ndx command (let’s say s_atom.ndx)

then use command for msd:
gmx msd -f md.xtc -s md.tpr -n s_atom.ndx -o msd.xvg

3

You can generate the index file of the molecules surrounding the S atom with gmx select tool and specifying the -on flag. However, if you reference a frame, then you will have the molecules surrounding atoms S at the time of the frame, then they may (or may not) diffuse around, depending on the nature of what you are looking at.