[gmx-users] 2016.3 only gmx grompp error on NVT step for ions

[Justin Lemkul]

On 1/23/18 12:21 PM, Sarai G wrote:
> ​Hello Justin,
>
> Sorry about the subject line, I fixed it this time around.
>
> I have the .itp files (toppar folder) and the .top files as you requested
> as well as a larger tar.gz which all of the files produced in the testing
> run within it.

The error message refers to line 14 because that is the last line in the 
topology; it does not indicate a problem with ions. That's a bit 
cryptic, but grompp is essentially just reporting that it has found a 
generic problem with your approach after processing all of the molecular 
topologies.

The simple solution to your problem is to not constrain all bonds, just 
h-bonds. I don't think OPLS requires all bonds to be constrained, just 
those to H.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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