[gmx-users] Nonbonded parameters

Justin Lemkul jalemkul at vt.edu
Wed Jun 12 14:22:20 CEST 2013

On 6/12/13 8:16 AM, Steven Neumann wrote:
> So how come 1830 1-4 interaction? There should be 57 of 1-4 interactions....

Mark already told you this - interactions that exist are different from possible 
interactions.  You may have 57 interactions, but that's specific to your system 
because of how many atoms there are (which is also independent of how many atom 
types are used therein).  grompp generates a bunch of information (a matrix of 
possible interactions that could theoretically occur with N atom types); whether 
or not it uses that information is not necessarily relevant.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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