Thanks (again) Olaf and Tristan for your last responses. Without using the vmd-plg.tcl file, I can use "pbc wrap" command in VMD.
However, still I can not get what I need. I need/want to visualize all the molecules in just one vesicle/aggregate but still the molecules are splitting (they are no broken) because of the periodic boundary conditions.
I took a look to two similar problems in vmd mail-list a) http://cvs.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/12052.html b)http://cvs.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/13992.html
So, after reading the suggestions what I tried was: pbc set "35.0 35.0 35.0" -all set box0 [pbc box_draw -shiftcenterrel "0 0 0" ] and one of the following commands: pbc wrap -center com -all pbc wrap -center com -compound chain -all pbc wrap -center com -compound res -all pbc wrap -center bb -compound res -all pbc wrap -center bb -compound chain -all
Also I tried using set sel [atomselect top all] and then pbc wrap -centersel $sel -center origin -compound res -all
But without success. I was wondering if a combination of "join" and "pbc wrap" could work. I tried but again I failed to wrap all the molecules in one aggregate Any last suggestion?