GROMACS version: 2019.2
GROMACS modification: Yes/No
Hi All,
My simulation started with surfactant molecules distributed randomly in water. At about t=200ns, the surfactants formed a micelle (i.e., a cluster). This micelle then remained stable through the rest of the simulation (another 500ns). I would like to analyze the portion of the trajectory from 200-700ns through which the micelle remained stable, and compute properties like the radius of gyration. However, the micelle does split across the simulation-box in some frames of the trajectory. I understand that I first need to make sure that the cluster remains ‘together’ through all the frames, otherwise, the radius of gyration will show unreasonable peaks.
I followed the steps given on this page Visualization Software — GROMACS 2021.1 documentation. However, since my micelle was formed at around the 200ns mark, and not in the first frame itself, I tweaked the steps given on the webpage a little. These are the steps I followed:
-
I first dumped out the frame at t=200ns
gmx trjconv -f original.xtc -s original.tpr -o dump_200.gro -dump 200000 -pbc whole -
I changed the timestep of this frame to t=0
gmx trjconv -f dump_200.gro -s original.tpr -o t0.gro -t0 0 -
I clustered and centered the micelle in this dumped out frame
gmx trjconv -f t0.gro -s original.tpr -n cluster0.ndx -o cluster.gro -pbc cluster -center yes -
I used this clustered.gro to create a new tpr
gmx grompp -f original.mdp -c cluster.gro -p topol.top -o cluster.tpr -
I then extracted the trajectory starting from t=200ns, and changed the time-stamp of the initial frame in this extract to ‘0’
gmx trjconv -f original.xtc -s original.tpr -o extract.xtc -t0 0 -b 200000 -pbc whole -
I then applied -pbc nojump to the extracted trajectory with the newly created tpr
gmx trjconv -f extract.xtc -s cluster.tpr -n cluster0.ndx -o cluster.xtc -pbc nojump -center yes
Please may I know from the community if my approach is alright? I would really appreciate any pointers from you all.
Thank you,
Sincerely,
Anu.