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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