Hi, > I'm still not clear what "sampling" means. Does it mean collecting data > from the simulation?
Pretty much. The point of a molecular dynamics simulation is to calculate structural, thermodynamic, etc... properties of some system from the microscopic dynamics of atoms/molecules/whatever. Collecting this information from the simulation is "sampling" that property from its overall distribution. Typically, the longer you simulate, the better your sampling is, but this isn't *always* true or feasible (e.g., development of enhanced sampling methods to speed this process up). By the way, the majority of the questions you have asked could probably be answered much quicker and more in-depth if you just searched for them on Google or took a look in the GROMACS manual. A massive amount of effort has been put into tackling the MD "sampling problem", so you'll find lots of information immediately. Best, John -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
