[gmx-users] Nonbonded parameters

Justin Lemkul jalemkul at vt.edu
Wed Jun 12 11:44:48 CEST 2013

On 6/12/13 5:30 AM, Steven Neumann wrote:
> Dear Gmx Users,
> Please, correct me if I am wrong. In ffnonbonded.itp
> [ atomtypes ] - these are nonbonded parameters between atoms of the same
> type

No, these are the nonbonded parameters that are used when applying combination 
rules between any atoms.

> [ nonbond_params ] these are nonbonded parameters between atoms of
> different type

No, these override combination rules.

> [ pairtypes ] - 1-4 interactions
> If that is correct why amber force filed has only [atomtypes] column? How
> nonbonded parameters are calculated between atoms of a different type?
> The same with charmm - only [atomtypes ] and [pairtypes ] are provided.
> Would you please explain?

Gromos force fields, for instance, have complex ways of generating nonbonded 
interactions that are not always the same for a given atomtype.  Other force 
fields just use straight combination rules and thus never need [nonbond_params].



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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