I am very new to Avogadro, so pardon any lack of understanding. I am attempting to use Avogadro to visualize a polymer network produced by a self-written MD code. It is a coarse-grained model, so the atom types I have used are abitrary. The output consists of bead co-ordinates and connectivity, which I wrote into a .cml file.
I am having some problems representing bonds which cross the periodic boundary of my cell. Must I duplicate the cells in the .cml file to show these bonds, or is there a way to wrap the bonds around using a unit cell? Also, is there a way to define the unit cell in a .cml file instead of going through the GUI? Very much appreciative of any help. ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
