[gmx-users] Re: Simulation of 2D lattice model
jmsstarlight at gmail.com
Sat Jan 5 07:45:08 CET 2013
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
C 6 0.000 0.000 A 0.0023406244 4.937284e-06
so it may complicate such correction in that ff.
2013/1/4, Justin Lemkul <jalemkul at vt.edu>:
> On 1/4/13 5:01 AM, James Starlight wrote:
>> 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
> 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
>> 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
> be calculated by combination rules. In this section, you can specify
> 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 A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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