[gmx-users] Nonbonded parameters

[Steven Neumann]

On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>

I read it.
I used combination rule 1 in which C=4epsSig^6 and A=4epsSig^12 - So that
means that when you provide in [atomtypes] in ffnonbonded your C and A
values each atom has a specific LJ potential shape. Right?
So two of them approaching each other in my system will have have the sum
of it.

Steven



>
>
>> 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
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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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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