What does it mean by a "site" in the case of a coarse-grained (CG) model in the above article?

Plz, describe it in layman's terms.

  • $\begingroup$ Related both Nike and Camp's answers. $\endgroup$
    – Tyberius
    Jun 1, 2022 at 3:09
  • 2
    $\begingroup$ I am not sure why you are calling TIP5P a course grained model. It is an atomistic model. $\endgroup$
    – B. Kelly
    Jun 1, 2022 at 11:04
  • $\begingroup$ I think "site" refers to the number of charges in the model. You can reproduce the charge of a molecule with a single charge; two charges allows you to also reproduce its dipole moment. As you add more charges, you can capture higher-order multipoles, anisotropy etc better, and if you allow the charge locations to move you can also start to model polarisability. $\endgroup$ Jun 1, 2022 at 15:32
  • $\begingroup$ A general definition would be a site of interaction - but in the case of water models, typically the sites refer to charges, since the number of atoms are fixed at 3. en.wikipedia.org/wiki/Water_model has pictures $\endgroup$
    – B. Kelly
    Jun 1, 2022 at 15:51

1 Answer 1


As the comments have already noted, a site in an atomistic model is the location in space at which interactions occur. The most obvious thing to do is to place all interaction sites at the atomic centers. This is exactly the case for TIP3P. That is, there are fixed charges placed on the oxygen and hydrogen atoms.

TIP3P did not do particularly well at modeling many properties of water, so TIP4P added another interaction site, which is slightly displaced from the oxygen atom along the HOH bisector. So, there are the three atomic interaction sites plus a fourth one which is usually called the M-site. The idea is that this fourth one is closer to the center of charge and hence might better capture the multipolar interactions. Because one is interested in the forces on a particular atom, one must then redistribute the forces at this M-site onto the atoms.

TIP5P just adds another M-site. From what I've heard, TIP5P is actually not much of an improvement at all over TIP4P and is more expensive, so TIP4P is usually preferred over TIP5P.

As an aside, the same principle can be used for polarizable force fields. For instance, many polarizable force fields for water place the polarizable centers off of the actual oxygen atom.

For the most part, I think only water models go to the trouble of placing interaction sites off of the actual atoms. With larger molecules, it would be rather tedious and possibly unnecessary to go to this trouble.

  • $\begingroup$ Are site and bead synonymous in the case of CG? $\endgroup$
    – user366312
    Jun 1, 2022 at 17:41
  • $\begingroup$ @user366312 my understanding is that "CG bead" and "CG site" are used interchangeably. $\endgroup$
    – Tyberius
    Jun 1, 2022 at 19:43
  • $\begingroup$ @Tyberius, then, I think, this answer needs an update. $\endgroup$
    – user366312
    Jun 1, 2022 at 20:11

You must log in to answer this question.

Not the answer you're looking for? Browse other questions tagged .