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

[Justin Lemkul]

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

-- 
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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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