Greetings to everyone!
I’m trying to find some information about neighbours list for VdW interactions creating principle in DL_POLY Classic. As far as I know, there are several ways to consider Van der Waals interactions in literature; for example:
- 1-2 case: all atom pairs that are directly connected via a linear bond will be excluded from VdW interactions list;
- 1-3 case: all 1-2 pairs will be excluded along with all pairs of atoms that are bonded to a common third atom (i.e., if atom A is bonded to atom B and atom B is bonded to atom C, then the atom pair A-C would be excluded);
- 1-4 case: all 1-3 pairs will be excluded along with all pairs connected by a set of two bonds (i.e., if atom A is bonded to atom B, and atom B is bonded to atom C, and atom C is bonded to atom D, then the atom pair A-D would be excluded);
- scaled 1-4 case: all 1-3 pairs are excluded and all pairs that match the 1-4 criteria are modified with the scaling factor. For example, this factor is equal to 0.5 in OPLS force field.
The DL_POLY Classic manual says, that the scaling factor can be defined for the scaled 1-4 case, if there is a dihedral angle specified. But what if the structure (and the FIELD file) doesn’t contain any dihedral angles potentials? Which case of considering the VdW interactions and creating of the neighbors list for it is used in DL_POLY Classic?
Any help would be appreciated.
Dear Petr,
Your question about van der Waals (vdW) interactions is not clearly formulated. In general, vdW interactions are defined between all non-bonded species, as opposite to chemically bonded species in, e.g., molecules. And the standard way for vdW interaction lists since 1967 is the Verlet method (Verlet list). Application of non-bonded interactions to atomic species in the same molecule are subject to special artificial ‘rules’, and are force-field (FF) dependant. Empirical FF are basically many-dimensional fits of the potential energy in the respective hyperspaces, and there is little physics in this procedure, but rather art and convenience. The reason for various treatments of ‘1-4’ interactions is the differences in developer preferences, the way how they see of how much of ‘non-bonded’ contribution should be mixed with ‘chemistry’. One cannot double count the same interaction, even under the different guises. The ‘1-2’, ‘1-3’, and ‘1-4’ lists are usually handled by different means from vdW interactions, and have meaning only when the system contains ‘molecules’. So, to answer your question, if there are no dihedrals in the system (e.g., only molecules with no more than 3 atoms), then there are no ‘1-4’ terms, and there is no scaling problem. Simple.
In DL_POLY 4 (or 5) and DL_POLY Classic there are different strategies for vdW interactions: DLP_Classic uses Verlet list, while DL_POLY 4 and above uses spatial (domain) decomposition – completely different strategy.
Hope this helps,
Vlad
Vlad, thanks a lot, the question became more clear for me. But what if, for example, the system contains big “molecule” (crystal), but no dihedrals are specified, and there are only chemical bonds, regular angles, long-range and short-range interactions in the force field? Is there a scaling problem in this case?
пн, 2 авг. 2021 г., 11:49 Vlad Sokhan - STFC UKRI <[email protected]>:
Hi Petr,
Well, the answer to your question would be “it depends…” – specifically, it depends on the FF used. The ‘1-4’ scaling is requested not by DL_POLY (or other MD software), but by the very fact whether it was provisioned in the FF by its developers in the first instance. You should consult the FF description, I believe. If it was, the only way to include the scaling in DL_POLY I could see is to define the whole system as one molecule (nummols 1) and atoms = [total number of atoms in the system]. Then, the ‘1-2’ interactions should be set to the interactions specified in the FF (in that case there is no distinction between ‘intra’ and ‘inter’ atomic interactions). I would not discuss the angle potential without seeing the specific FF: too many options here. Scale the ‘1-4’ interactions according to FF requirements, and use the same potential as for ‘1-2’ for vdW interaction – these will kick in (in full) starting from ‘1-5’ neighbours. However, it is likely that the scaling was not intended in the FF, in that case use ‘intramolecular’ terms from the FF (for the ‘1-2’ and ‘1-3’) and set the scaling factor for ‘1-4’ to 1.
It’s really difficult to say something more definite without seeing the FF in question.
Best,
Vlad
The fact is that I’m not using the “existing” or published FF, but trying to construct one myself. And to correctly create the optimizing algorithm (i.e. correctly obtain VdW parameters), I need to know, how the VdW neighbors list is created in the MD simulation package I want to use (in this case - DL_POLY Classic). At this stage of work I use only chemical bonds, regular angles, long range and short range interactions in the FF. The approximate template of the FIELD file I use:
UNITS eV
MOLECULES 1
Molecule_name
NUMMOLS 1
ATOMS 5440
atom_1 mass charge
…
atom_5440 mass charge
BONDS X
HARM atom_i atom_j parameter_1 parameter_2
…
MORS atom_k atom_l parameter_1 parameter_2 parameter_3
…
HARM atom_x atom_z parameter_1 parameter_2
…
ANGLES Y
HARM atom_i atom_j atom_k parameter_1 parameter_2
…
FINISH
VDW Z
atom_type1 atom_type1 lj parameter_1 parameter_2
…
atom_type_n atom_type_m lj parameter_1 parameter_2
…
CLOSE
Of course, parameters are unique in each particular case.
Really appreciate your help.
пн, 2 авг. 2021 г. в 16:48, Чекушкин, Пётр Михайлович <[email protected]>: