[gmx-users] Re: Simulation of 2D lattice model
jalemkul at vt.edu
Fri Jan 4 21:32:29 CET 2013
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 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
> 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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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