improper cvff

Dear lammps users,

Is the position in which the central atom in the IJKL important ?

For eg., from lammps manual, I is the central atom in IJKL (assume I forms a bond with J K L).

If the central atom is atom is K (assume there is a bond between KJ, KL, KI) can one still use improper cvff with the same IJKL ordering ?

I used edihed to check and I observed there is change in energies when one switches the ordering of the central atom.

I am not sure how the improper style estimates the angle between the planes.

Does it use the bond information in any way ?.

Thanks

1 Like

Which improper style are you asking about? I believe
the doc page for each improper style (also see the doc
page for improper_style command itself), discusses
the correct ordering for the 4 atoms. And yes, it does
matter, i.e. it changes the computation.

Steve

Dear lammps users,

Is the position in which the central atom in the IJKL important ?

If the central atom is atom is K (assume there is a bond between KJ, KL,
KI) can one still use improper cvff with the same IJKL ordering ?

I think so, yes. (See below.)

For eg., from lammps manual, I is the central atom in IJKL (assume I forms
a bond with J K L).

I used edihed to check and I observed there is change in energies when one
switches the ordering of the central atom.

And yes, it does
matter, i.e. it changes the computation.

Actually, this is tricky.
When you swap the order of the J,K atoms, the angle between the IJK
and JKL planes, (φ), remains the same, except for a change in sign (φ
-> -φ). In the specific case of improper_cvff, the energy should not
change (because the energy, which depends on cos(n*φ)). I am inclined
to guess that most (if not all?) improper styles currently implemented
in LAMMPS are unaffected when you swap the J and K atoms (but I
confess I'm to lazy to check).

Arun, if you are getting different energies, I suspect you changed the
atom ordering elsewhere (such as the atom ordering in the dihedral
interactions). Note: To calculate the improper energies, you should
be calculating "eimp", not "edihed".

  --- More generally ---

My impression is that improper interactions are normally used as a
constraint to enforce co-planarity (ie to force these 4 atoms to lie
in the same plane). In that case, it is not important whether "J" or
"K" is the central atom. Because if the improper forces are strong
enough (ie. if the "k" coefficient is large enough), then these four
atoms will be forced to lie within the same plane regardless of which
atom is the central atom.

(If either angle, φ or -φ equals 0, then both are 0.)

Summary: Regardless of which improper_style you use, it should not
really matter. But in your case (using improper_style cvff), then it
should not matter at all.

I am not sure how the improper style estimates the angle between the
planes.

typically by calculating the dot-product between the normal-vector of
the two planes (each calculated using the cross-product)

Does it use the bond information in any way ?.

No. I don't think any of the bonded interactions care about how the
atoms are bonded together. (Including improper, dihedral, or angle
interactions).

(Details: If you look at the LAMMPS source code, the list of bonds is
saved in the atom->bond_atom array, but the code which calculates
improper interactions does not seem to refer to this array:
grep "bond_atom" improper_*.cpp # try this in "src/")

According to the documentation for improper_style cvff:

"If the 4 atoms in an improper quadruplet (listed in the data file
read by the read_data command) are ordered I,J,K,L then the improper
dihedral angle is between the plane of I,J,K and the plane of J,K,L.
Note that because this is effectively a dihedral angle, the formula
for this improper style is the same as for dihedral_style harmonic.
Note that defining 4 atoms to interact in this way, does not mean that
bonds necessarily exist between I-J, J-K, or K-L, as they would in a
linear dihedral. Normally, the bonds I-J, I-K, I-L would exist for an
improper to be defined between the 4 atoms."

So it does not matter how atoms I,J,K,L are bonded together

Feel free to correct me if I'm wrong about anything I said.
Improper-forces are confusing to me too.

Cheers

Andrew

Dear lammps users,

Is the position in which the central atom in the IJKL important ?

If the central atom is atom is K (assume there is a bond between KJ, KL,
KI) can one still use improper cvff with the same IJKL ordering ?

I think so, yes. (See below.)

My apologies. I did not read your email carefully enough.

And yes, it does
matter, i.e. it changes the computation.

Oops. Yeah, Steve's right.

If you assume "I" is the central atom (instead of "K"), then yes, you
will definitely get totally different angles. For some reason, I
thought the question concerned swapping "J" and "K". (Swapping J and
K does not effect the magnitude of the φ angle.) Please ignore this
part of my email.

However, since you are only using improper interactions as a
constraint to enforce co-planarity, then, in practice, either
convention can be successful at accomplishing this task (depending on
the choice of parameters). This is definitely the case when using
improper_style cvff with n=2.

Andrew

P.S.
Incidentally, this is how moltemplate implements the AMBER/GAFF
force-field. For details, see:
http://structbio.vanderbilt.edu/archives/amber-archive/2007/0408.php
The "n=2" setting comes directly from gaff.dat.