On 6/12/13 6:00 AM, Steven Neumann wrote:
Thank you. That means that e.g. when two LJ atoms of a different type
approaching each other the non bonded LJ potential energy is a sum of two
potentials of those atoms?
No, please refer to the Gromacs manual for discussion on "combination rules" and
how they fit into the Lennard-Jones equation.
-Justin
On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul <jalem...@vt.edu> wrote:
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
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Department of Biochemistry
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Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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