variable pebig equal pe*atoms/count(big)
In the examples given under SRD, the calculation of potential energy for big particles is given as
Here, do 'atoms' stand for the total number of atoms in the system? If yes, is this more of an average value of the PE of group big? Isn't there a way to get the pe of a certain group?
My other question is, I am calculating the vacf and mean square displacement as well using the fixes specifically for group big. Do I need to do this averaging for that as well? This is what I mean:
compute msd all msd
variable msdbig equal msd*atoms/count(big)
or can I just calculate that by doing the following:
compute msd big msd