GROMACS version: 5.1
GROMACS modification: Yes/No
I have run this command for no pbc gmx trjconv -s md_0_10.tpr -f md_0_10.xtc -o md_0_10_noPBC.xtc -pbc mol -center, but after this I get a trajectory file in which ligand is moving out of protein. What can be the reason behind it. How can I solve this problem?
why it hasnot been centered even after centering pbc commands?
Ligand moving out after no pbc gmx trjconv -s md_0_10.tpr -f md_0_10.xtc -o md_0_10_noPBC.xtc,reason
What group did you choose for centering?
As mentioned in tutorial I have selected 1 i-e protein for centering and 0 i-e system for output.
Moreover, I have also checked and visualized npt. gro nvt.gro and all gro files but in all these files ligand remains inside protein only in md trajectory it moved out as shown above, what can be solution to this problem?