SRD energy calculations


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.