[gmx-users] Question regarding nrexcl and gen-pairs for angle terms with incomplete bonds (ClayFF)

Thomas Underwood thomas.underwood at princeton.edu
Tue Oct 3 00:29:53 CEST 2017

Hi Matt, thanks a bunch for your response.

I'm still slightly unsure that this would work as you describe it. If I set nrexcl = 0, then the non bonded interactions between all neighbours will be included. (Though, the fudge factors = 0 then cancel this out?)

The problem comes from the fact that I don't want the non bonded interactions between hydroxyl atoms in my simulations, but I do need the other nearest neighbour interactions included.

In my example, I have the triplet {i,j,k}. Let's say that i is my hydrogen, j is my oxygen, and k is my metal (Al/Mg) atom.
I need the non bonded interactions between my metal atom and the oxygen atom included in my simulation (j & k), as well as the non bonded interaction between the metal and the hydrogen (i & k). I need to exclude the non bonded interaction between the hydrogen and the oxygen (i & j).

So far, I've assumed that if I declare a bond between my hydrogen and oxygen, but not between the oxygen and metal atom, then my non bonded interaction between oxygen and metal remain included in the simulations.
I suppose the key question is... does the inclusion of the angle term change the non-bonded interactions between atoms i and k, even though I don't have a bond defined between atoms j and k.
Is the nearest neighbour list build up exclusively from bonds, or does gromacs use angles (and dihedrals) to also build up its neighbour list.



On 2 Oct 2017, 18:10 -0400, Thompson, Matthew White <matt.thompson at vanderbilt.edu>, wrote:
The normal use (nrexcl = 3 and fudgeQQ & fudgeLJ > 0) results in GROMACS removing 1-2, 1-3, and 1-4 non-bonded interactions and then adding back scaled to the numbers given. In ClayFF, as I understand it, there is no such exclusion of these 1-x interactions and therefore no 1-4 scaling. If you want 1-2 non-bonded interactions to be included, which it seems you do, you can set to set nrexcl = 0. In this case, it is still possible for there to be bonded interactions between the 1-2 pair independent of whether or not the non-bonded interactions are included. But I don't think you want any pairs, as you're not "adding back" any scaled 1-4 or other interactions, so you would want to set fudgeQQ and fudgeLJ = 0. Otherwise some interactions will be double-counted (or 1.5x counted). I have used nrexcl = 0 and fudge = 0 for a similar system based on ClayFF and found that was the only way to get data to agree with other simulation engines, whereas other setups would cause the system to
crash. I'm pretty sure any other combination will cause interactions to be counted incorrectly with respect to ClayFF.


From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Thomas Underwood [thomas.underwood at princeton.edu]
Sent: Monday, October 02, 2017 3:02 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Question regarding nrexcl and gen-pairs for angle terms with incomplete bonds (ClayFF)

Dear GMX'ers,

I have a brief question regarding the use of nrexcl and gen-pairs when used with a non-bonded forcefield, such as ClayFF. I've had a brief look through previous posts but haven't found a completely satisfactory answer.

Currently, I have a system that is entirely non-bonded. The exception to this is hydroxyl groups.
In addition, there is an angle term between the hydroxyl group and an adjacent metal atom.
I'm wondering what implications this angle term has on the nonbonded interactions of my system.

Let's say I have a triplet of atoms: {i,j,k}.
I define a bond between atoms i and j; I have an angle defined between i, j, and k; but I have NO angle defined between j and k.

Now, if I set nrexcl = 1, will the nonbonded interaction between j and k still be present in my simulation? I.e. does the angle term at all affect the outcome of my pair interactions?

Overall, I need nonbonded interactions between atoms {i,k} and {j,k} in this setup.

Further, gen-pairs is typically used for 1-4 interactions. However, when I set nrexcl less than 3, does this also generate 1-3 interactions, such as the one between i and k above?

Thanks in advance,


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