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

[James Starlight]

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
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.


James


2013/1/3, Justin Lemkul <jalemkul at vt.edu>:
>
>
> On 1/3/13 2:01 PM, James Starlight wrote:
>> Justin,
>>
>> 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
> ffnonbonded.itp.
>
> -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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