questions on MB-pol/MB-nrg

[Young In Jhon]

Hello?

I'd like to ask some questions about MB-pol/MB-nrg for my deep understanding of MB-pol/MB-nrg.

1. My understanding is that point charges are located H1,H2, and M sites while induce dipoles are located in L1,L2,and O sites of a monomer water in MB-pol.
It seems that intramolecular interaction are considered only among induced dipoles of individual water molecule (not for all intramolecular interaction among 6 sites of a water molecule).
Is it right?


2. For ion (Li+,Cl- etc.) and water interaction, what types of electrostatic points and what their values are used for ions in MB-nrg?
Is it right that only point charges are considered (without considering induce dipoles) and their values are +1 or -1?
Otherwise, how charge values should be determined for ions?

 
3. There are many file names (A1_B1, A1_B2, grad, nograd etc.) in potential/2B as shown below.

x2b-A1B2Z2_C-v1x.cpp
poly-2b-A1B2Z2_C-v1x.cpp
poly-2b-A1B2Z2_C-v1.cpp
poly_2b_A1B2_A1B2_v1x.cpp
poly_2b_A1B2_A1B2_v1.cpp
x2b_A1B2_A1B2_v1x.cpp
x2b_A1B2Z2_C1D2_v1x.cpp
poly_2b_A1B2Z2_C1D2_v1x.cpp
poly_2b_A1B2Z2_C1D2_v1.cpp
poly_2b_A1B4_A1B4_deg4_exp0_v1.cpp
poly_2b_A1B4_A1B4_deg4_exp0_v1x.cpp
x2b_A1B4_A1B4_deg4_exp0_v1x.cpp
x2b_A1B2Z2_C1D4_deg3_exp0_v1x.cpp
poly_2b_A1B2Z2_C1D4_deg3_exp0_v1x.cpp
poly_2b_A1B2Z2_C1D4_deg3_exp0_v1.cpp
poly_2b_A2_A2_deg6_nograd_v1.cpp
poly_2b_A2_A2_deg6_grad_v1.cpp
poly_2b_A1B2Z2_C2_deg5_nograd_v1.cpp
poly_2b_A1B2Z2_C2_deg5_grad_v1.cpp
poly_2b_A1_B1C2X2_deg5_nograd_v1.cpp
poly_2b_A1_B1C2X2_deg5_grad_v1.cpp
poly_2b_A1_B2_deg7_nograd_v1.cpp
poly_2b_A1_B2_deg7_grad_v1.cpp
poly_2b_A1_A1_deg9_nograd_v1.cpp
poly_2b_A1_A1_deg9_grad_v1.cpp
poly_2b_A1_B1_deg9_nograd_v1.cpp
poly_2b_A1_B1_deg9_grad_v1.cpp
x2b_A1B2C4_D1E2_deg3_v1x.cpp
poly_2b_A1B2C4_D1E2_deg3_v1x.cpp
poly_2b_A1B2C4_D1E2_deg3_v1.cpp
poly_2b_A1B3_A1B3_deg4_grad_v1.cpp
poly_2b_A1B3_A1B3_deg4_nograd_v1.cpp


However, the meaning of name is difficult to know and confusing.
Would you let me know what's the nomenclaturerule rule and/or meaning of  thier names in detail?
To see final energy and/or force expression of 2B potential (I suppose it would be something like product sum of functions (return values) described in these files), what file should we check?


4. For 1B, I suppose that the potential form of Partridge and D. W. Schwenke is used in MB-pol as it is (without any change).
Is it right?
To see final energy and/or force expression of 1B potential (I suppose it would be something like product sum of functions (return values) described in these files), what file should we check?


Thank you for your answers in advance.

  Luke

[Marc Riera]

Hello, I insert answers:

On Tuesday, August 2, 2022 at 10:13:42 AM UTC-4 Young In Jhon wrote:

Hello?

I'd like to ask some questions about MB-pol/MB-nrg for my deep understanding of MB-pol/MB-nrg.

1. My understanding is that point charges are located H1,H2, and M sites while induce dipoles are located in L1,L2,and O sites of a monomer water in MB-pol.
It seems that intramolecular interaction are considered only among induced dipoles of individual water molecule (not for all intramolecular interaction among 6 sites of a water molecule).
Is it right?

The sites, positions and usage of the MB-pol model are deeply explained in https://pubs.acs.org/doi/full/10.1021/ct400863t and in the SI. Long story short, M site is used in electrostatics only, while L1 and L2 are just two extra sites used by the polynomials only to describe and mimic the position of the lone pairs of water. Intramolecular induced dipoles are allowed as long as the external field comes from atoms not in the same water molecule.

 

2. For ion (Li+,Cl- etc.) and water interaction, what types of electrostatic points and what their values are used for ions in MB-nrg? 

All the monomers in MBX (and within the MB-nrg framework) are always the same, no matter to what are they interacting with. This means that water is still a 4-point monomer (OHHM), and is exactly the same as the one used for water-water interactions. 

 

Is it right that only point charges are considered (without considering induce dipoles) and their values are +1 or -1?

We do not use point charges, but smeared charges (see TTM4 - Thole type model 4 electrostatics for more details). Our electrostatics model is a slight modification of the TTM4 model (changed some damping parameters)

 

Otherwise, how charge values should be determined for ions?

The charges come from ab initio calculations, either CHELPG or CM5 charge calculation. For monoatomic ions, the answer is pretty trivial since they can only have a total charge of 1 or -1, but for molecules such as CO2, CH4 and so on, one needs to perform a population analisys to get the atomic charges.

For this it depends. What is the purpose of that? What do you want to do/check? Depending on the answer, one needs to look at different places, although the code is not set up to just obtain those values. MBX will return the total energy of the system, and the gradients if specified.

 

4. For 1B, I suppose that the potential form of Partridge and D. W. Schwenke is used in MB-pol as it is (without any change).

Is it right? Correct

To see final energy and/or force expression of 1B potential (I suppose it would be something like product sum of functions (return values) described in these files), what file should we check?

You can decompose your system and calculate the individual energy of each water molecule. Add all numbers together and you will have the total 1b energy.

 

Thank you for your answers in advance.

No problem, hope this helped!

 

  Luke