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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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