Greetings,
I am trying to use MSI InsightII to do MD studies on some small
sugar-like gelators. I would like to be able to monitor
intermolecular hydrogen-bonding throughout the simulation, but I'm not
sure if, or how, I can do this. I started out just modeling a few
molecules in a cell and had planned to monitor the distances between
the hydrogen bonding sites, but this isn't a great way to do it, and
furthermore with the PBC, sometimes one of the molecules will start to
interact with a "neighbor" instead of the other molecules, which
defeats the purpose of my distance monitors. If anyone has any
suggestions or advice for someone new to MD, I would be most
appreciative.
Thanks.
