Post MD simulation Visualizations

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
Here post your question

gmx trjconv -s MD.tpr -f MD.xtc -o MD_center.xtc -center -pbc mol -ur compact -dt 10 (stride by 10 step)
#Choose “Protein” for centering and “System” for output.

#To extract the first frame (t = 0 ns) of the trajectory, use trjconv -dump with the recentered trajectory:
gmx trjconv -s MD.tpr -f MD_center.xtc -o start.pdb -dump 0

I used this command to center my multichain protein, but when I load the file in VMD, the peptide chains move outside the PBC and appear stretched.

2

Hi deep_1,

try to use the option -pbc cluster for multimers. That also worked for the simulations of an homotrimeric protein, I recently performed.

Best regards,

Benedikt

3

Thank you. The peptide chains remained intact, but the dimers were observed to move away from each other. Is this normal?