[gmx-users] Re: Simulation of 2D lattice model

[James Starlight]

Justin, thanks for explanation again!

So if I understood correctly in the  ffnonbonded c6 correspond to the
attraction term and c12 to the repulsion term doestn't it ?  So might
the vdw radius of the atom be increased/ deacreased via corrections in
the c6 term ?

            mass charge ptype       V(c6)      W(c12)
 O    8 15.99940  0.000     A 0.22617E-02 0.74158E-06

by the way I've found that in all gromos ff both C6 term given in the
inapropriate form

C    6 	0.000      0.000     A  0.0023406244  4.937284e-06

so it may complicate such correction in that ff.


James

2013/1/4, Justin Lemkul <jalemkul at vt.edu>:
>
>
> On 1/4/13 5:01 AM, James Starlight wrote:
>> Justin,
>>
>>
>> thanks again for explanation.
>>
>> I've tried examine that parameters more carefully. E.g in my system
>> with 2 atom types I defined in topology
>>
>> [ atomtypes ]
>> ;name  at.num   mass      charge ptype       c6           c12
>>    CH2    6 	0.000      0.000     A  0.0023406244  4.937284e-06 ; CB
>>    CH1    6 	0.000      0.000     A  0.0023406244  4.937284e-06 ; CA
>>
>>
>> where both C6 and c12 values were coppied from simple C (carbon atom)
>> ;    C    6 	0.000      0.000     A  0.0023406244  4.937284e-06
>>
>> As I understood c6 correspond to the Rmin (sigma) term in LJ equation
>> andc 12 is the pre-exponential (eps) factor which correspond to the
>
> Not directly.  One can convert between C6/C12 and sigma/epsilon fairly
> easily
> but it is not true that C6 = sigma and C12 = epsilon.  See, for instance,
> http://en.wikipedia.org/wiki/Lennard-Jones_potential#AB_form and manual
> section
> 5.3.2.
>
>> potential dept. So why addition
>> [ nonbond_params ] are needed where such interactions are presence for
>> pair of that atoms ?
>>
>
> The [nonbond_params] directive overrides the interactions that would
> otherwise
> be calculated by combination rules.  In this section, you can specify
> special
> interaction potentials between atomtypes.
>
>> ; i    j func          c6           c12
>> ; CH3      CH2  1  0.008473481  3.0084136e-05
>>
>> In particular I'd like to change vdw radius for the selected atoms of
>> my lattice ( by adding a new type for such atoms).
>>
>> 2) Could you also provide me some examples of the editconf parameters
>> for box vectors and angles for definition of the new box types ? In
>> particular I'd like to build pyramide-like box with the truncated top
>> (like in the Maya's ancient temples) for my lattice.  I've not found
>> any reasonable tutorial for that.
>>
>
> I have no experience building such things.  Maybe someone else can help you
> do that.
>
> -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
>
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