Without any additional information, I would strongly suggest that you use PBC. This is the standard way to conduct simulations of dense liquids, which I presume you have as your water bath that is surrounding the protein and nanoparticle.
If you are doing this in vacuum for some reason then you don't need PBC. There are tricks that avoid using PBC, but they are not all available in gromacs (charmm has more tricks in this regard) and they are all intended to reduce the computational requirements at the expense of a poorer representation of the solvent. If you have some specific reasons why you think that your system is particularly suitable to simulation in the absence of PBC, then you should tell us what it is. Chris. -- original message -- I want to simulate gold nanoparticle interaction by a protein. Due to the use of PBC to get closer to the state of the bulk, who knows for this simulation whether I should use pbc or not? thanks Fatemeh Ramezani -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
