Hi all, <br>I am trying to use *trjconv command for -pbc but POPC molecules are breaking when visualize in VMD. The commands used are <br>grompp -f pr.mdp -c em_out.gro -p .top -n index.ndx -o out.tpr<br>trjconv -f em_out.gro -s out.tpr -o trj_out.gro -pbc inbox or cluster or whole<br>
Thi trj_out.gro contain broken POPC molecules <br>Pls suggest me what options I have to use for -pbc? or any addition option I have to use?<br>Thanks in advance.......<br>