Hello Janne, this is what I usually do when my molecules cross the box or dance all around and it works for me:
I first do this with the "original" unmodified or fitted xtc or trr file: trjconv -f -o -pbc nojump then i take the modified trr or xtc and do a fit: trjconv -f -s -fit rot+trans Belquis > Hello gmx-users! > > I am trying to make a simulation video in which a water droplet is > rolling or sliding on a surface. Due to a periodic boundary conditions > a droplet is not whole all the time but it disappears from the right > and appears from the left in cycles. > > I think that I could create more visual video by removing the lateral > motion of the center of mass of a droplet so that the droplet would > stay whole > in the middle of simulation window and the surface would translate > below the droplet. I am not exactly sure how realistic this kind of > video would be and would like to know if someone has better ideas? > > If there are no better ideas I would need advices to be able to create > a such trajectory or video. Right now I am struggling with trjconv > which might be suitable for this purpose. However, if I use the > droplet as a group for translational fit (-fit translation) I get > trajectory in which the whole system wanders strangly (laterally (the > surface moves first to the left and then back to the right) and also > in perpendicular to the surface due to the lowering of the height of > the center of mass of the droplet during the simulation) and the > droplet wont stay whole in the middle of the box. Any ideas what I am > doing wrong or how I would be able to get rid of even this lateral > wandering so that I could at least see how realistic this procedure is? > > > Thanks for your time and help in advance, > > Janne > > > ------------------------------------------------------------------------------ > Janne Hirvi, MSc(Physical Chemistry), Researcher > University of Joensuu, Department of Chemistry, P.O.Box 111 80101 Joensuu, > FI > Tel: +358 13 2514544 & +358 50 3474223 > E-mail: [EMAIL PROTECTED] & [EMAIL PROTECTED] > ------------------------------------------------------------------------------ > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > > > _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
