[gmx-users] Nonbonded parameters
Steven Neumann
s.neumann08 at gmail.com
Wed Jun 12 12:00:22 CEST 2013
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?
On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul <jalemkul at 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
>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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