[gmx-users] nrexcl for TIP4P-ICE water model

[Justin Lemkul]

On 2/6/20 2:18 PM, mbhendle wrote:
> Hello all,
>
> I want to use tip4p-ice water for my simulations and the tip4p-ice
> topology  "_tip4p-ice.itp_" (i am using )is same as:
>
> http://www.sklogwiki.org/SklogWiki/index.php/GROMACS_topology_file_for_the_TIP4P/Ice_model
> [1]
>
> Is nrexcl=1 correct ???
> As the other topologies (eg. spc, spce, tip4p) in oplsaa have nrexcl=2.
> Will it affect my results.

The value of nrexcl is made irrelevant in that topology by the 
subsequent definition of [exclusions] for all possible intramolecular 
interactions.

> As nrexcl is used to set 1-4 non-bonded interactions on/off and water
> does't have any.

The value of nrexcl sets the distance in terms of bonds for the excluded 
interactions; it is not only applicable for excluding 1-4 interactions. 
In conventional biomolecular force fields, nrexcl=3 does exclude 
interactions within 3 bonds. But you can set the value (in principle) to 
anything you want. As water cannot have 3 consecutive bonds, the proper 
value to exclude all intramolecular interactions is 2.

-Justin

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Justin A. Lemkul, Ph.D.
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