[gmx-users] [ defaults ] and nonbonded

[Steven Neumann]

Whether it would be that easy i will find it. I specified my own potential
(not LJ) - so how come I should choose option 1 or 2 in nbfunct? I changed
h(x) in my table 6th column.


On Wed, Jun 12, 2013 at 1:18 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/11/13 4:12 PM, Steven Neumann wrote:
>
>> Dear Gromacs Users,
>>
>> I got really confused: In manual [defualts ]:
>>
>> "nbfunc is the non-bonded function type. Use 1 (Lennard-Jones) or 2
>> (Buckingham)"
>>
>> I want to use mdrun -table table.xvg with my own potential, which one I
>> should choose?
>>
>> "gen-pairs - is for pair generation. The default is ‘no’, i.e. get 1-4
>> parameters from the pairtypes list. When parameters are not present in the
>> list, stop with a fatal error. Setting‘yes’ generates 1-4 parameters that
>> are not present in the pair list from normal Lennard-Jones parameters
>> using
>> fudgeLJ"
>>
>> I want to have all intramolecular atoms (within my chain) interacting (no
>> exclusions) with each other from [ atomtypes ] in ffnonbonded.itp
>> Does it mean "yes" with nrexcl =1 in my topology?
>>
>> And sth I also got confused:
>>
>> [ pairtypes ] are only 1-4 parameters or here I can specify parameters for
>> all atoms within my molecule? So [ atomtypes ] in ffnonbonded.itp also
>> correspond to intra molecular interactions?
>>
>>
> These topics are discussed frequently.  Please search the archive; surely
> you will find relevant topics.
>
> -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://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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