[gmx-users] Re: Simulation of 2D lattice model
jmsstarlight at gmail.com
Fri Jan 4 11:01:57 CET 2013
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
potential dept. So why addition
[ nonbond_params ] are needed where such interactions are presence for
pair of that atoms ?
; 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.
2013/1/3, Justin Lemkul <jalemkul at vt.edu>:
> On 1/3/13 2:01 PM, James Starlight wrote:
>> thanks again for explanation. By the way if I define in topology top
>> LJ params like
>> ; Include forcefield parameters
>> #include "gromos53a5.ff/forcefield.itp"
>> [ atomtypes ]
>> ;name at.num mass charge ptype c6 c12
>> CH2 6 0.000 0.000 A 0.0074684164 3.3965584e-05
>> CH3 6 0.000 0.000 A 0.0096138025 2.6646244e-05
>> [ nonbond_params ]
>> ; i j func c6 c12
>> CH3 CH2 1 0.008473481 3.0084136e-05
>> [ moleculetype ]
>> ; Name nrexcl
>> ICE 3
>> i've obtain warns
>> WARNING 1 [file lattice.top, line 23]:
>> Overriding atomtype CH2
>> WARNING 2 [file lattice.top, line 24]:
>> Overriding atomtype CH3
>> does it mean that the params from topology.top will be used instead of
>> RTP file ?
> Not from the .rtp file, but the .top is overriding the contents of
> 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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