[gmx-users] Nonbonded parameters

[Justin Lemkul]

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 <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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-- 
========================================

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

========================================