GROMACS version: 2018
GROMACS modification: No
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.
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.