Yes, I know what you mean - I keep meaning to make a modified trjconv where '-fit trans' only affects the xy coordinates, for my bilayers, but it never quite seems important enough. If your droplet moves at a constant rate, trjconv -shift will, I think, move the coordinates by an amount proportional to the framenumber (so at a constant speed) and then all you'd have to do is play with the periodicity. Never tried it though. If you're making the movie with VMD (unpretty, but functional) you can control the periodic imagery quite well in a manner that may help.
----- Original Message ---- From: "[EMAIL PROTECTED]" <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Tuesday, September 25, 2007 4:03:17 PM Subject: [gmx-users] Pbc and Com in simulation video 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 gmx-users@gromacs.org 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 ____________________________________________________________________________________ Take the Internet to Go: Yahoo!Go puts the Internet in your pocket: mail, news, photos & more. http://mobile.yahoo.com/go?refer=1GNXIC _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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