Sometimes, it is helpful to get the index (number starting from zero) or serial (number starting from one) for the currently drawn part of the molecule in vmd. For example, it you want to create an index file for a given system, or if you want to split up your […]
VMD
3 posts
Sometimes, one has the bond topology but not the matching angle or dihedral definitions. Here is how to get them in VMD with topotools.
In case you observe strange (long distance) bonds while animating a trajectory with VMD, this might be due to rearrangements of the molecule structure during the animation’s time frame. Sometimes, this behavior is not useful – especially, if you have lots of those conformation variations. In order to disable the […]