Improper atom order incorrect in LAMMPS data writer for harmonic impropers?

[rsdefever]

Bug summary

It appears that the atom ordering for harmonic impropers is incorrect in the LAMMPS data writer. Here is the code that writes the impropers. Note that the atoms are written so that the atom1.idx is written in the third position.

            # Dihedral data
            if impropers:
                data.write("\nImpropers\n\n")
                for i, improper in enumerate(impropers):
                    data.write(
                        "{:d}\t{:d}\t{:d}\t{:d}\t{:d}\t{:d}\n".format(
                            i + 1,
                            improper_types[i],
                            improper[2],
                            improper[1],
                            improper[0],
                            improper[3],
                        )
                    )

However, LAMMPS specifies that the central atom should be first see docs here, and parmed stores the central atom first see docs here.

Am I missing something, or are we reordering these atoms when we should not be.

[ahy3nz]

I can't really remember how I came to that conclusion in an old PR

[rsdefever]

@ahy3nz thanks for hopping in here. I guess we need to make some simple test cases to throw through parmed. The parmed docs are either wrong, or something has changed.

[rsdefever]

Unless someone beats me to the punch, I'm going to create a test case with formic acid. Its a small and simple molecule. I'll make up a fake improper if I have to and I'll create two XMLs; one with a harmonic improper and one with an amber-style improper. Then we can look at the parmed.Structure and also write to LAMMPS, GROMACS, Cassandra, (and others?) and see what happens. 😬 😬 😬

[mattwthompson]

Impropers are a complete and utter mess. Everybody does it a little differently, everybody adds their own quirks, nobody can agree on the right ordering. I can go on but we're all familiar with the idea.

I don't trust anything short of running an MM single-point energy and isolating just the improper contribution to the overall potential energy. Absolutely tedious but I don't think there's any shortcuts to be had here. LAMMPS and GROMACS make it feasible enough to decompose potential energy contributions (with some file parsing), and I'm assuming Cassandra does as well. CHARMM might, Amber probably does, but OpenMM doesn't.

In fact, OenMM's grouping of propers and impropers has probably led to some confusion in Foyer - are there impropers here? I don't know. ParmEd will probably find some, and plausibly be correct about them, but it's hard to verify them without understanding the source of the data (which I do not).

[rsdefever]

Impropers are a complete and utter mess.

Agreed, but we're stuck with them 👎 .

Here is a gist with an XML file that has an amber-style improper and a python script for formic acid. Please don't take it too seriously. Its a bit of a frankenstein file, but will work for this purpose. Am I being dumb or can we even specify harmonic impropers with foyer?

All I've looked at so far is writing parmed -> gmx. The central atom (c) appears to be written 3rd. Can anyone find a reliable source to say whether that is correct or not for gromacs? I didn't see it mentioned in the reference manual, although I feel like it must be there. Here and here is a start. This thread from the mailing list seems to say central atom should be first?

Update: For formic acid and with amber-style impropers parmed appears to be storing the central atom third in the improper. This is consistent with the parmed docs for amber-style impropers here.

import foyer
import mbuild
import parmed

mol = mbuild.load("C(=O)O", smiles=True)
ff = foyer.Forcefield("improper_amber.xml")

mol_ff = ff.apply(mol)

mol_ff.save("test.gro", overwrite=True)
mol_ff.save("test.top", overwrite=True)

impropers = [d for d in mol_ff.dihedrals if d.improper]
print(impropers[0].atom3.idx) # this atom is index 0, the central atom.

# Just to double check that loaded parmed from file gives the same
# result as using foyer -> parmed
mol_loaded = parmed.load_file("test.top", xyz="test.gro")

impropers = [d for d in mol_loaded.dihedrals if d.improper]
print(impropers[0].atom3.idx) # this atom is index 0, the central atom.

So for amber-style impropers, parmed definitely storing central-atom-third. This is consistent with the docs.

The open question is then for harmonic impropers. The parmed docs say central atom first. I'll update when I learn more.

[rsdefever]

Update: I've done a simple test. Take a gro/top/mdp file. Remove the proper dihedrals. Copy the improper dihedral -- switch it from an "improper" to a "proper" -- type 4 to type 1. Keep the atom ordering the same in both, and compute the energy. The energy of the two dihedrals ("proper" or "improper") is the same when the central atom is 3rd. When the central atom is moved to the first position for the improper, the energy changes.

Files here.

[rsdefever]

Just to add more options for thinking about this...
here is a zip with a minimal working example in LAMMPS. LAMMPS very clearly specifies central atom first. The energy it gives is: 0.0678461708 kJ/mol when the central atom (c, 1-indexed atom 1) is placed first. This more or less agrees with the "flipped" energies from GROMACS.

[rsdefever]

First, apologies if anyone is confused by this thread. I have removed a few earlier comments because I felt that they were unnecessarily complicating the matter.

Harmonic impropers: I am going to compare manually computed energies with LAMMPS and GROMACS.

parmed preserves the harmonic improper order when reading/writing gmx files. For example, if the topology has an improper with the atoms listed in order 1 4 3 2, then the atom1.idx, atom2.idx, etc, in parmed have the same order. You can easily confirm this with the python script attached as part of gromacs_debug.tar.gz.

Next, if we trust the parmed docs, we know the central atom should be first. Then, we can calculate the energy of the improper. We can also flip the first and third atom and re-compute the energy.

Next, we can compute the energies of the original and flipped topologies with gmx. We can compare the energies between our values and theirs.

Finally, we can compute the improper energy in LAMMPS, which clearly defines central atom first.

Summary:
LAMMPS, GROMACS, and the manual calculation show very similar energies when central atom is first. This suggests that the parmed documentation is correct. It also suggests that our LAMMPS writer is incorrect. Please let me know if there is an error in my logic.

gromacs_files.tar.gz
lammps_files.tar.gz

Here are the results from the manual calculation:

(1-indexed) first atom in parmed improper is: 1
Harmonic improper energy is 0.06784616933084593 kJ/mol
(1-indexed) first atom in parmed improper is: 3
Harmonic improper energy is 20.18619305350575 kJ/mol

From GROMACS with this topology:

[ dihedrals ]
;    ai     aj     ak     al funct         c0         c1         c2         c3
      1      4      3      2     2    10.0000000     4.6024000

the energy is: Improper Dih. 0.0723808 -- 0 0 (kJ/mol)

For the flipped topology:

[ dihedrals ]
;    ai     aj     ak     al funct         c0         c1         c2         c3
      3      4      1      2     2    10.0000000     4.6024000

the energy is: Improper Dih. 20.1864 -- 0 0 (kJ/mol).

The energy from lammps is: 0.0678461 for the following impropers:

Impropers

1       1       1       4       3       2

[rsdefever]

@ahy3nz I agree with most of the observations in your comment. However, I disagree with:

Parmed Structure: A parametrized Structure will list the central atom as the third atom for ALL impropers.

As far as I can tell, the CHARMM-style (harmonic) impropers are stored central-atom-first. I make this statement based upon reading/writing GROMACS files, the documentation, and a comparison of the computed energies between by-hand, LAMMPS, and GROMACS.