SRD energy calculations

Hello,

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

Sincerely,

John

pe*atoms/count(big)

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.

Steve

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?

Thanks,

John

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.

Steve