<html><body><div style="color:#000; background-color:#fff; font-family:verdana, helvetica, sans-serif;font-size:12pt"><div>Dear GROMACS users</div><div><br></div><div>I want to analysis of 2 micelles that are created in one simulation, when I view output of trajectory by vmd or ngmx:</div><div>ngmx -f md.trr -s md.tpr</div><div>has been created 2 micelles, then I try to micelle clustering by: <br></div><ol><li><code>trjconv -f md.xtc -o a_cluster.gro -e 0.001 -pbc cluster</code></li><li><code>grompp -f md.mdp -c a_cluster.gro -o a_cluster.tpr</code></li><li><code>trjconv -f md.xtc -o a_cluster.xtc -s a_cluster.tpr -pbc nojump</code></li></ol><div><span></span></div><div>but when I view cluster.xtc, just has been created one micelles and remainder of monomers have been collected in different places in 3 or 4 groups!!!</div><div><br></div><div>May I know why do this occur? and where is my mistake? and what should I do, please?</div><div>Please help
me.</div><div><br></div><div>Best Regards</div><div>Sara <br><span></span></div><span class="meta-link"></span></div></body></html>