[gmx-users] Binary lennard jones

[Mark Abraham]

On 12/12/2010 6:25 PM, leila separdar wrote:
> yes I have read them many times

OK, so you know how to understand how your .top files are describing the 
nonbonded interactions between your atom types. Now you just need to 
combine the two. Probably you want one atomtypes section, etc. If you 
want them to interact, then you'll need to define parameters 
accordingly, either using combination rules (see manual) or with 
explicit nonbond_params (see manual).

Mark

> On Sun, Dec 12, 2010 at 10:41 AM, Mark Abraham 
> <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>> wrote:
>
>     On 12/12/2010 6:08 PM, leila separdar wrote:
>
>         I want to simulate a binary lenard jones system. I have .top
>         and .gro file for both A and B atom types . how can I mix this
>         two atom types ? do I must regard the lenard jones potential
>         between this two atom type or not? and where I must put C12
>         and C6 parameters for interaction between these two atoms?
>
>
>     Have you done the necessary background reading in chapters 4 and 4
>     of the manual?
>
>     Mark
>     -- 
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