[lammps-users] Setting the Amber FF torsion/dihedral paramter in lammps

LAMMPS LAMMPS Mailing List Mirror
1

Hi,

According to the example input script for using Amber FF (from the “README” file for the tool “amber2lmp”):

The dihedral style is “dihedral_style harmonic”.

However some torsion parameters I found from the Amber FF website contain the periodicity terms, which means there is a sum over “n” for the harmonic functional terms, where n = 1, 2, 3.

How can I input this periodicity into my lammps input script? Use “dihedral_style class2” and coeffs to be zeros for non-periodic torsions?

-Fei

2

I don't know. The formulas for the various dihedral options
in LAMMPS are all listed on the doc pages. If one of those
isn't what you want, then a new dihedral style would have to
be added. AMBER, CHARMM, etc have lots of variants. LAMMPS
surely doesn't support all of them.

Steve

3

I don't know. The formulas for the various dihedral options
in LAMMPS are all listed on the doc pages. If one of those
isn't what you want, then a new dihedral style would have to
be added. AMBER, CHARMM, etc have lots of variants. LAMMPS
surely doesn't support all of them.

quite often one can represent the periodicity requirements of the
amber or charmm force fields by defining the same dihedral multiple
times with different dihedral types and then have each type correspond
to one of the periodic components.

cheers,
   axel.

4

Hi, Axel,

Thanks for your reply.

Do you mean something like “dihedral_style hybrid”?

But, according to my understanding of the LAMMPS tutorial, if I define the same dihedral type multiple types, the latter one will overwrite the previous definition instead of the a sum of the two definitions?

Is it true?

-Fei

5

Hi, Axel,

Thanks for your reply.

Do you mean something like "dihedral_style hybrid"?

But, according to my understanding of the LAMMPS tutorial, if I define the
same dihedral type multiple types, the latter one will overwrite the
previous definition instead of the a sum of the two definitions?

Is it true?

what i wanted to suggest is to define each dihedral (in the data file)
multiple times and give each definition a different type. this way you
will not overwrite the types and can have a different set of parameters.

but while looking at the documentation for an input example, i saw that
LAMMPS has now a dihedral_style multi/harmonic and i suspect that
this would be the better solution (if you teach amber2lmp how to use
it that is).

cheers,
    axel.