Analysis and trajectory conversion

User discussions
1

GROMACS version: 2018
GROMACS modification: No

Dear all

I have simulated a membrane system using PBC and without giving any command for the removal of the center of mass in the mdp file. I would like to know generally for the analysis of this system, specifically the RDF and MSD analysis tools of GROMACS, should I use trjconv to convert the trajectory, and if so, which steps should I go through.

Thank you very much for your help.

Best,
Azadeh

2

Typically, gromacs does necessary trajectory conversion (e.g. -pbc whole/nojump), users do not need to do explicitly. There are few notes,

  • For COM based RDF, you need to have whole molecules. You can convert trajectory with -pbc whole, then do RDF. Check if you get similar answer without conversion.

  • For MSD calculation, The whole molecules should be unwrapped, Which can be achieved,

    • gmx trjconv -f .trr/.xtc -s *.tpr -pbc whole -o whole.gro
    • gmx trjconv -f whole.gro -s whole.gro -pbc nojump -o nojump.gro

Gromacs does this automatically, yet I would do it manually and check against unconverted trajectory.

  • Even though, you didn’t specify comm-mode/nstcomm, gromacs by default removes after every 100 steps. COM removal is necessary for MSD, otherwise you would get higher self-diffusion due to global motion arises from accumulation of kinetic energy.

Thanks
Masrul