[gmx-users] Nonbonded parameters

[Steven Neumann]

An why do I have 1830 non bonded? 60*60/2 = 1800. There are 57 of 1-4
combinations so it should be lower than 1800...
And why 1830 1-4 interactions as I have only 57... Please, help/

Steven


On Wed, Jun 12, 2013 at 11:40 AM, Steven Neumann <s.neumann08 at gmail.com>wrote:

> 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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>