In the examples given under SRD, the calculation of potential energy for big particles is given as
variable pebig equal pe*atoms/count(big)
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
means total PE of system * Natoms (in system) / Natomsbig (# of big atoms)
pe and atoms are thermo keywords (see the thermo_style command)
When this script does thermo output quantities are divided by Natoms
(default for LJ units), settable by themo_modify norm.
So you will effectively get the PE/big-atom, in an average sense.
If you want to sum the pe/atom for just big atoms, see the compute
reduce command. Or compute ke/atom or variable group function ke(group)
You can just use compute msd for a group of atoms (e.g. big). See its doc
page for an explanation.
Thank you for the reply. Additionally, is there a particular reason why for the pure SRD simulations, we used atom_style atomic and for the mixture simulation, style sphere is used? Since I want to use electric field, do I use atom_style hybrid with sphere and charge (or) dipole and charge (or) just charge?
SRD particles are point particles. Hence if you just
run an SRD fluid you can use atom_style atomic.
The mixture simulation adds finite size (colloidal) particles.
Hence you need atom_style sphere (which can also include
point particles). If you want charge in either case, then
you need atom_style charge (for point particles) or the
hybrid sphere + charge (you could also use sphere with
fix property/atom). For point dipoles, you would nee a hybrid
atom styyle that includes dipole.