OK I used the connect command and it works like a charm. I open the XYZ file and then load the script:
set autobond false; connect 2.65 (_Si) (_Si); connect 1.79 (_Si) (_H); connect 2.16 (_Si) (_N); connect 0.90 (_H) (_H); connect 1.18 (_H) (_N); connect 1.20 (_N) (_N); I think Jmol loops over all pairs of atoms and over all frames. This may take a while. One of my bigger systems contains 370 atoms and I have 500 frames ... It takes about 10 minutes but it works and I can play the animation. Thank you ! On Sun, 2009-03-22 at 09:56 +0100, [email protected] wrote: > Hi, > > I am trying to view a molecular dynamics simulation, where bonds are being > formed and destroyed. The data is in the XYZ format containing multiple > structures. However I would like to use my own cut-off distances for > bonds. > Is there a way to do this in Jmol ? > Are the bonds being evaluated at each MD step or just at the first one ? > > I was searching the documentation, but there I found that you can change > only Van der Vaals radius but not the covalent. > > Regards, > > Karol > > > ------------------------------------------------------------------------------ > Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are > powering Web 2.0 with engaging, cross-platform capabilities. Quickly and > easily build your RIAs with Flex Builder, the Eclipse(TM)based development > software that enables intelligent coding and step-through debugging. > Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com > _______________________________________________ > Jmol-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-users ------------------------------------------------------------------------------ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
