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

Justin Lemkul jalemkul at vt.edu
Tue Jan 23 19:05:15 CET 2018

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 

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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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