HI Gromacs Friends,<br> I complete one simulation for 4 different molecule placed apart <br>in box of dimension 4 4 4 ..<br>when I used the trajectory I saw the one molecule interact with each other but they are <br>
getting broken because of box..(Some part protruding from other side).<br>To see movie I used the command <br>1. trjconv -s ..tpr -f ..xtc -o movie.pdb -pbc nojump -dt 10 <br> The molecules moving apart without any interaction <br>
<br>2. trjconv -s ..tpr -f ..xtc -o movie.pdb -pbc whole -dt 10<br> The molecules are interacting in cell ..<br> but because of periodic cell , near the cell boundary the molecule <br> interaction get remove and molecules come in cell from other side..<br>
( I know it is because of periodic boundary condition ..one goes from right <br> hand side come in cell through left hand side )<br> <br>To see the four molecule interacting each other near also cell boundary , what command <br>
I have to use ???<br>