[gmx-users] Nonbonded parameters

Wed Jun 12 13:57:47 CEST 2013

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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