Hi,
I would like to run the MD simulation of a linear molecule and I came to know from the link mentioned below that a virtual construction site should be added in the topology to maintain perfect linearity.
http://chopra-modules.science.purdue.edu/class/chm579/spring2019/public/pages/vsites/01_intro.html
But I am confused that how can I generate the coordinate files (pdb) of such linear molecule using the dummy atoms? Can I able to do with the general software like Avogadro or Gauss view or need to do something else? It will be very helpful if anyone put some light on this.
Thanks in advance.
I don’t know whether standard tools can do this. Note that the actual values of the coordinates of the virtual sites are irrelevant, as they are constructed by mdrun. If you do need dummy masses, a normal input file will work.