<html><body><div style="color:#000; background-color:#fff; font-family:bookman old style, new york, times, serif;font-size:14pt"><div>Dear gromacs users,</div><div><br></div><div>At the first I thank from Tsjerk and Mark because of their answers to me but unfortunately I don't understand that where is my mistake, still?<br></div><div>I work with MARTINI coarse-grained and I have a problem after -pbc nojump! My simulation lasts 600 ns and 2 micelles are created from 200 ns and
remain during 400 ns, then my micelles isn't formed at the end of the <span class="yshortcuts" id="lw_1325238252_0">trajectory.</span></div><div>My commands are:</div><div>1- trjconv -f md.trr -s md.tpr -n index.ndx -e 600000 -pbc cluster -o 1.gro</div><div><span class="yshortcuts" id="lw_1325238252_0"> In this step I viewed 2 micelles from 200 ns to 600 ns by ngmx -f 1.gro -s md.tpr, so I have 2 micelles and -pbc cluster works me well and has been removed box boundaries from my system but I saw very jumps in my system. Okay?<br></span></div><div><span class="yshortcuts" id="lw_1325238252_0">2- grompp -f md.mdp -c 1.gro -o 1.tpr -n in</span><span class="tab">dex.ndx</span></div><div><span class="tab">3- trjconv -f 1.gro -s 1.tpr -o 2.xtc -pbc nojump</span></div><div><span class="tab">After this step, had been removed jumps but I didn't see 2 micelles in 200 ns, I saw that my monomers were collected as groups in the different places. (This is bad and
I don't know where is my mistake and what should I do to solve my problem!)</span></div><div><span class="tab">After this, to solve my problem, I did:</span></div><div><span class="tab">4- trjconv -f 2.xtc -s 1.tpr -o 3.xtc -pbc mol <br></span></div><div><span class="tab">In this step, I viewed 2 micelles from 200 ns to 600 ns and had been removed jumps but existed boundaries of box, means my micelles </span>that leaves a simulation box by, say, the right-hand face, then enters the simulation box by the left-hand face. <br></div><div>May I know can I start analysis of my system with 3.xtc? Is it good? If it isn't good, Please help me for this problem with nojump.</div><div><br></div><div>Thank you very much in advance</div><div>Best Regards</div><div>Sara<br></div></div></body></html>