Opening Centre of Mass (COM) dump file in VMD

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1

Dear Lammps User,

I have just written out the Centre-of Mass (COM) coordinates for the molecules in my simulation using:

compute cc1 all chunk/atom molecule
compute myChunk all com/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector

The intention is to use this to get the radial distribution function, g® on VMD as I have read here. The problem I have is that VMD cannot directly open this file. Please how can I get this done? Thank you very much.

2

Dear Lammps User,

I have just written out the Centre-of Mass (COM) coordinates for the
molecules in my simulation using:

compute cc1 all chunk/atom molecule
compute myChunk all com/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector

The intention is to use this to get the radial distribution function, g(r)
on VMD as I have read here. The problem I have is that VMD cannot directly
open this file. Please how can I get this done? Thank you very much.

this is not a LAMMPS question, but a VMD question. you should post
these kind of questions on the VMD mailing list.
the *very* obvious answer is: write a little tool, that converts the
output you have into a file format that *is* by VMD.
for details on that, you *definitely* should read the VMD docs and ask
further questions on the VMD mailing list.

axel.

3

Thank you for your response earlier, I have requested for subscription to the VMD mailing list.

I have a question concerning the dump file used by these blocks of codes:

compute cc1 all chunk/atom molecule ids once

compute myChunk all com/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector

compute mychunk all chunk/atom molecule ids once
compute msd all msd/chunk mychunk
fix 2 all ave/time 1000 1 1000 c_msd[*] mode vector file msd.data

I have a heterogeneous mixture of molecules and want to calculate the diffusion coefficient and RDF for molecules of the same type. Now, it seems from what I have read here that LAMMPS can’t identify what molecules belongs to what component (that is, LAMMPS can’t tell if it is a benzene or naphthalene molecule). Or maybe I’m wrong.

Can you please point me in the right direction to do this calculation? Thank you very much.