Hi Sara, Please keep discussions on the list. I'm not your private tutor.
Whether you can do your analysis depends on the analysis you want to do. But if your aim is analyzing the formation of the micelle, you're probably better of reversing the trajectory. > 1- trjconv -f md.trr -o md1.xtc -n index.ndx -pbc whole -s md.tpr This makes molecules whole, which is fine. Clustering should make molecules whole too, though, making this step redundant. > 2- trjconv -f md1.xtc -s md.tpr -o cluster1.gro -e 600000 -pbc cluster Fine, you get a cluster > 3- trjconv -f cluster1.gro -s md.tpr -dump 150 -o cluster2.gro This does nothing special. Just because you have a reference clustered doesn't mean the output frame will turn out clustered. > 4- grompp -f md.mdp -c cluster2.gro -o cluster1.tpr -n index.ndx > 5- trjconv -f cluster1.gro -o cluster1.xtc -s cluster1.tpr -pbc nojump This screws up everything. You can only use -pbc nojump with a reference structure that is sufficiently close to the first frame of the trajectory. Your reference is a snapshot at t=600 ns. > 6- trjconv -f cluster1.xtc -s cluster1.tpr -pbc mol -ur compact -center -o > cluster3.xtc This would probably be fine if the trajectory was okay there. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
