[gmx-users] Nonbonded parameters

[Steven Neumann]

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>
>
> ==============================**==========
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>