[gmx-users] Nonbonded parameters

Justin Lemkul jalemkul at vt.edu
Wed Jun 12 14:08:07 CEST 2013 

On 6/12/13 8:01 AM, Steven Neumann wrote:
> 60 types of atoms and 60 atoms in total belonging to one residue

The number of possible combinations is (N(N+1))/2, thus you get 1830 from 60 
atom types.

-Justin

>
>
> On Wed, Jun 12, 2013 at 12:59 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:
>
>> How many atom *types* are there?
>>
>>
>> On Wed, Jun 12, 2013 at 1:57 PM, Steven Neumann <s.neumann08 at gmail.com
>>> wrote:
>>
>>> and 1830 1-4 interactions... there are "57 all possible 1-4 interactions"
>>>
>>>
>>> On Wed, Jun 12, 2013 at 12:55 PM, Steven Neumann <s.neumann08 at gmail.com
>>>> wrote:
>>>
>>>> "All possible interactions = 60*60/2 = 1800. Where grompp takes another
>>> 30
>>>> from?
>>>>
>>>>
>>>> On Wed, Jun 12, 2013 at 12:52 PM, Mark Abraham <
>> mark.j.abraham at gmail.com
>>>> wrote:
>>>>
>>>>> "Parameters for possible interactions" is not the same as
>>> "interactions."
>>>>> The latter depend on the configuration and cut-offs... grompp is not
>>> doing
>>>>> a neighbor search!
>>>>>
>>>>> Mark
>>>>>
>>>>>
>>>>> On Wed, Jun 12, 2013 at 1:48 PM, Steven Neumann <
>> s.neumann08 at gmail.com
>>>>>> wrote:
>>>>>
>>>>>> On Wed, Jun 12, 2013 at 12:45 PM, Mark Abraham <
>>>>> mark.j.abraham at gmail.com
>>>>>>> wrote:
>>>>>>
>>>>>>> grompp is just enumerating the possible combinations of parameters
>>>>> given
>>>>>>> your inputs. Whether any of those will be used in the simulation
>>> will
>>>>>>> depend on whether atoms of given types are close enough and not
>>>>> excluded.
>>>>>>>
>>>>>>> Mark
>>>>>>
>>>>>>
>>>>>> I understand...but why for 60 mer polypeptide there are 1830
>> nonbonded
>>>>>> interactions ?
>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Wed, Jun 12, 2013 at 12:40 PM, 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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-- 
========================================

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

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