[gmx-users] gold nanoparticle simulation,use pbc or not?

Christopher Neale chris.neale at mail.utoronto.ca
Tue Sep 11 04:34:48 CEST 2012

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.


-- 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?
Fatemeh Ramezani

More information about the gromacs.org_gmx-users mailing list