MSD calculation with or without mol option for a group of large molecules

User discussions
1

GROMACS version: 2081.8
GROMACS modification: No

Hello,
My system contains one kind of relatively large molecules since each of them has 31 atoms. There are about 25-150 molecules in the system along with other components. If I want to use gmx msd to get the MSD of this particular group, could you please tell me whether the -mol option should be used or not? I have read the manual but do not understand it fully.

  • My understanding is that with -mol option, it will output the diffusion coefficient of each molecule in this group. But what would be the basic difference for the MSD results of this whole group? I have tried with groups of this large molecule and water molecules, for water molecules, the differences in the MSD of the whole group are negligible, but for the group of this large molecule, the difference is not significant but is obvious.
  • For a relatively large molecule, I think it is possible that it is not moving that much, but could rotate around an almost fixed point, should the MSD caused by this kind of movement be excluded in the MSD calculation?
  • I found that with -mol options, the usage of the memory becomes much much higher, could you please also explain the reason?
    Any help would be much appreciated!