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.
Cheers,
Tom
On 2 Oct 2017, 18:10 -0400, Thompson, Matthew White
<[email protected]>, 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.
Matt
________________________________________
From: [email protected]
[[email protected]] on behalf of Thomas
Underwood [[email protected]]
Sent: Monday, October 02, 2017 3:02 PM
To: [email protected]
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,
Tom
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