<html><body><div style="color:#000; background-color:#fff; font-family:bookman old style, new york, times, serif;font-size:14pt"><div><span>Thank you very much from your reply.</span></div><div><br></div><div>Best Regards</div><div>Sara<br></div> <div style="font-family: bookman old style, new york, times, serif; font-size: 14pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <font face="Arial" size="2"> <hr size="1"> <b><span style="font-weight:bold;">From:</span></b> Tsjerk Wassenaar <tsjerkw@gmail.com><br> <b><span style="font-weight: bold;">To:</span></b> mohammad agha <mra_bu@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Thursday, December 29, 2011 1:56 AM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] -pbc nojump<br> </font> <br>
Hi Sara,<br><br>Please keep discussions on the list. I'm not your private tutor.<br><br>Whether you can do your analysis depends on the analysis you want to<br>do. But if your aim is analyzing the formation of the micelle, you're<br>probably better of reversing the trajectory.<br><br>> 1- trjconv -f md.trr -o md1.xtc -n index.ndx -pbc whole -s md.tpr<br><br>This makes molecules whole, which is fine. Clustering should make<br>molecules whole too, though, making this step redundant.<br><br>> 2- trjconv -f md1.xtc -s md.tpr -o cluster1.gro -e 600000 -pbc cluster<br><br>Fine, you get a cluster<br><br>> 3- trjconv -f cluster1.gro -s md.tpr -dump 150 -o cluster2.gro<br><br>This does nothing special. Just because you have a reference clustered<br>doesn't mean the output frame will turn out clustered.<br><br>> 4- grompp -f md.mdp -c cluster2.gro -o cluster1.tpr -n index.ndx<br>> 5- trjconv -f cluster1.gro -o cluster1.xtc -s cluster1.tpr -pbc
nojump<br><br>This screws up everything. You can only use -pbc nojump with a<br>reference structure that is sufficiently close to the first frame of<br>the trajectory. Your reference is a snapshot at t=600 ns.<br><br>> 6- trjconv -f cluster1.xtc -s cluster1.tpr -pbc mol -ur compact -center -o<br>> cluster3.xtc<br><br>This would probably be fine if the trajectory was okay there.<br><br>Cheers,<br><br>Tsjerk<br><br>-- <br>Tsjerk A. Wassenaar, Ph.D.<br><br>post-doctoral researcher<br>Molecular Dynamics Group<br>* Groningen Institute for Biomolecular Research and Biotechnology<br>* Zernike Institute for Advanced Materials<br>University of Groningen<br>The Netherlands<br><br><br> </div> </div> </div></body></html>