[gmx-users] How could I know whether I should use epsilon-sigma or c6-c12?

[Mark Abraham]

On 5/06/2012 5:04 PM, Bao Kai wrote:
> Hi, Mark,
>
> The values of c6-c12 parameters are different from the values of
> epsilon and sigma, and they can be converted to each other.
>
> My point is which values I should specify in my .top file.  Or it does
> not matter totally and Gromacs will determine what kinds of values you
> are specifying.

You determine it with your force field's [defaults] directive. See 
various parts of chapter 4 and 5, particularly the worked example in 
chapter 5.7.1.

Mark

>
> Thank you.
>
> Kai
>
> On 5/06/2012 4:34 PM, Bao Kai wrote:
>> Hi, all,
>>
>> I am still trying to do my simulation with liquid mixtures.
>>
>> I have a simple question now. When I writing my .top file, how could I
>> know if I should use epsilon-sigma or c6-c12 parameters for the LJ
>> potential? It seems that in some examples, c6-c12 parameters are used
>> and epsilon-sigma parameters are used in some other examples.
> The model you are implementing chooses this and the rule by which
> parameters of different atom types get combined into interaction type
> parameters. The rationale for that choice often seems vague, IMO
> probably doesn't matter much, and is not really your problem until you
> go to design models. Literature is your friend, here.
>
> Mark