[lammps-users] Parameters and units generated using msi2lmp tool

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1

Dear LAMMPS users,
I am trying to carry out MD simulations on cross-linked epoxy polymer system. I have used Materials Studio to build the polymeric system and exported it to .car and .mdf file. These files were then used to build the LAMMPS input file using msi2lmp tool of Laamps-17Nov16 version. I have used cvff force field to generate the input file.
My doubt is regarding what are the units in the generated input file.

For example, the input for EPON molecule looks like

LAMMPS data file. msi2lmp v3.9.8 / 06 Oct 2016 / CGCMM for MSMSE-epon
53 atoms

54 bonds
94 angles
130 dihedrals
12 impropers

9 atom types
13 bond types
22 angle types
26 dihedral types
3 improper types

-7.440362581 7.433742905 xlo xhi
-4.870577406 4.955093769 ylo yhi
-2.685406512 2.685535778 zlo zhi

Masses

1 15.999400 # oh
…
…
9 1.007970 # ho

Pair Coeffs # lj/cut/coul/long

1 0.2280000124 2.8597848722 # oh
…
…
9 0.0000000000 0.0000000000 # ho

Bond Coeffs # harmonic

1 384.0000 1.4200 # oh-c1
…
…
13 363.4164 1.0800 # cp-h

Angle Coeffs # harmonic

1 58.5000 106.0000 # c1-oh-ho
…
…
22 60.0000 120.0000 # o-cp-cp

Dihedral Coeffs # harmonic

1 0.1300 1 3 # ho-oh-c1-c3
…
…
26 3.0000 -1 2 # o-cp-cp-h

Improper Coeffs # cvff

1 0.3700 -1 2 # c-cp-cp-cp
2 0.3700 -1 2 # cp-cp-cp-h
3 0.0000 -1 2 # o-cp-cp-cp

What I know is the unit of Mass mentioned in ’ 1 15.999400 # oh’ is amu.
The unit of Bond Coeffs mentioned in ‘1 384.0000 1.4200 # oh-c1’ is Kb kcal/mol/sq. Ang and b0 is Ang.

Please clarify the units of angle energy, dihedral energy, improper energy and pair potentials generated.
More clarifications on this will be really helpful.
Thanks in advance.

Regards,
Sindu

2

The energy units are specified in the units command (for example, units real will mean energy is specified in kcal/mol), and angle units are specified in the particular angle_style (etc) command.

For example angle_style harmonic specifies angles in degrees, so the angle energy constant is in [energy units]/degree/degree. I can’t imagine any style using any angle units besides degrees – but just check the documentation.

Cheers
Shern

3

Unrelated to your questions, you are using an over 5 year old version of an actively maintained software. Don’t you think it would be wise to upgrade to a recent version to benefit from bugfixes and improvements?

What you are looking at is the “data file”, but the most important settings and hints to the answers you are looking for are in the “input file” that is also generated by msi2lmp. That will contain the units command setting and the various force field styles to be used. The details of the units and parameters you can then look up in the manual based on that information.

4

Hi Axel,

In your previous reply regarding the .in file, you wrote:

‘What you are looking at is the “data file”, but the most important settings and hints to the answers you are looking for are in the “input file” that is also generated by msi2lmp. That will contain the units command setting and the various force field styles to be used. The details of the units and parameters you can then look up in the manual based on that information.’

I checked the documentation, but couldn’t find the feature to generate the Lammps .in file, as you mentioned.

Many thanks for your advice.
Best wishes

Lili

5

I must have confused msi2lmp with charmm2lammps.
Sorry about that. I use neither program regularly and LAMMPS has many tools and commands, so mixing similar things up is always a problem.