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From: |
Steve Plimpton <sjplimp@...24...> |

Date: |
Tue, 13 Jun 2017 08:36:19 -0600 |

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

On Mon, Jun 12, 2017 at 5:31 PM, John Smith <johnson21smith@...24...> wrote:

JohnHere, 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?Hello,In the examples given under SRD, the calculation of potential energy for big particles is given asvariable pebig equal pe*atoms/count(big)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 msdvariable msdbig equal msd*atoms/count(big)or can I just calculate that by doing the following:Sincerely,compute msd big msd

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**Follow-Ups**:**Re: [lammps-users] SRD energy calculations***From:*John Smith <johnson21smith@...24...>

**References**:**[lammps-users] SRD energy calculations***From:*John Smith <johnson21smith@...24...>

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