[gmx-users] Nonbonded parameters

[Steven Neumann]

I got it. However,

I have 60  atoms in my chain all with given C6 and C12 with a combination
rule 1. When running grompp:

Generated 1830 of the 1830 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 1830 of the 1830 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_X'
Analysing residue names:
There are:     1    Protein residues
Analysing Protein...
Number of degrees of freedom in T-Coupling group rest is 118.00
This run will generate roughly 2 Mb of data

when changing nrexcl in my topology to 0:


Generated 1830 of the 1830 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 1830 of the 1830 1-4 parameter combinations
Excluding 0 bonded neighbours molecule type 'Protein_chain_X'
Analysing residue names:
There are:     1    Protein residues
Analysing Protein...
Number of degrees of freedom in T-Coupling group rest is 118.00
This run will generate roughly 2 Mb of data

So if I exclude 1-3 interactions I have the same number of nonbonded
parameters as well as 1-4 interactions. Can someone explain me this please?



On Wed, Jun 12, 2013 at 11:12 AM, Steven Neumann <s.neumann08 at gmail.com>wrote:

>
>
>
> 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
>>>> Blacksburg, VA
>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>> http://www.bevanlab.biochem.****vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
>>>> <h**ttp://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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>
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