Hi, it is basically a hit and trial thing, where you test different lag times and see at what lag-time, the convergence is achieved and explains the kinetic of the system.

There is a discussion at this page:

https://github.com/Acellera/htmd/issues/230

and here is a tutorial, where they discuss how to build, have a look and hopefully you will get an idea of how to select lag time:

http://msmbuilder.org/legacy/tutorial.html

Hope it will be helpful.