On the preprocessing and post-processing with lammps

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1

Hi, all,

I come back again.

I am still trying to do some simulations with the CO2 and water
mixture ( maybe some ions later).

I did not find any good tutorials that can help me go through a whole
simulation process and I have two quick questions now.

1. How can I generate the initial positions for the molecules of the
mixtures? Is there some supportive command provided by lammps? If not,
how the people usually do that with lammps?

2. When I finish some simulations, how can I do the analysis with the
simulated results. For example, how can I get the density, diffusion
coefficient and viscosity of the mixtures.

I have read some books on molecular simulations, and I have the basic
knowledge now. I have chosen the required molecule models. For the
force field, it seems that only a few force fields are supported in
lammps, right? Or basically, I can use any force field model by
providing the parameters?

Thank you very much.

Best Regards,
Kai

2

Comments below.

Steve

Hi, all,

I come back again.

I am still trying to do some simulations with the CO2 and water
mixture ( maybe some ions later).

I did not find any good tutorials that can help me go through a whole
simulation process and I have two quick questions now.

1. How can I generate the initial positions for the molecules of the
mixtures? Is there some supportive command provided by lammps? If not,
how the people usually do that with lammps?

For molecular systems you need a builder of some sort. Other MD
codes have these; LAMMPS does not. But you can take
output files from those codes and convert them to LAMMPS input.
There are several LAMMPS tools for this. See the doc/Section_tools.html
page,

2. When I finish some simulations, how can I do the analysis with the
simulated results. For example, how can I get the density, diffusion
coefficient and viscosity of the mixtures.

You can compute them on-the-fly with LAMMPS (fix ave/spatial,
compute msd, see Section 6.21 of the manual for viscosity options).
Or you can post-process LAMMPS dump files to calculate
whatever you want.

3

Comments below.

Steve

Hi, all,
I come back again.
I am still trying to do some simulations with the CO2 and water
mixture ( maybe some ions later).
I did not find any good tutorials that can help me go through a whole
simulation process and I have two quick questions now.
1. How can I generate the initial positions for the molecules of the
mixtures? Is there some supportive command provided by lammps? If not,
how the people usually do that with lammps?

For molecular systems you need a builder of some sort. Other MD
codes have these; LAMMPS does not.

There are several examples of how to build a system of water mixed
with salt ions or with hydrocarbons at http://moltemplate.org.
Section 3 of the manual shows how to build a box of water, and one of
the examples in the "examples" directory explains how to mix two
different types of molecules together (in that case water and salt
ions). Moltemplate will build the geometry, topology, and assign
force-field parameters to the water at least. You will have to create
your own molecule template for CO2. (In the future, if I ever get
GAFF assignment working, then perhaps you won't have to do this
either. This is a ways off, however.)
Please email me if you have questions.

4

Hi, Steve,

Thank you very much for your response. I will try to finish my first
lammps simulation.

Kai

5

Hi, Andrew,

This is pretty useful. I will try it.

Thank you.

Kai