[gmx-users] soft core potential

[Erik Lindahl]

Hi,

No - the sigma value will be the default sc_sigma since c6 was zero.

Actually, the sigma in the softcore equations is just an interaction 
lengthscale that could be completely separate from the actual LJ 
interaction parameters c6/c12. In practice it is convenient to 
calculate it from the LJ parameters if they are availabe, so that's 
what everybody does unless c6 or c12 is zero.

Think of it this way:

1. First we calculate or assign the length sigma. In most cases it is 
smart to use c6/c12 to derive a reasonable length, but it doesn't 
really relate to the LJ interaction. If we cannot derive it, use 
sigma=sc_sigma.
2. Forget that this value of sigma might have been derived from c6/c12 
- it is only a rough approximation anyway.
3. Use the calculated value of sigma for the soft-core distortion of 
potentials, including LJ interactions if c6 or c12 is non-zero.

If c12>0 and c6=0, the default sc_sigma will be used to distort the 
repulsive potential. The dispersion interaction is zero with c6=0.

Cheers,

Erik





On Monday, October 6, 2003, at 02:03 PM, Ilya Chorny wrote:

> More specifically. My C12 term has a positive value. My C6 term is 0. I
> am only concerned with the C12 term which is
> C12/(alpha*sigma^6*lambda^2+r^6)^2
> but the sigma value must be C12/C6 which if C6 was zero would blow up.
> Does gromacs set the C6 value to sc_sigma^6.
>
> Ilya
>
>
> If the soft core used a value of zero then it would blow up. What
> On Mon, 2003-10-06 at 13:37, Erik Lindahl wrote:
>> Hi,
>>
>> As a said in the last paragraph - if c6=0 there isn't any dispersion
>> interaction at all, neither distorted or normal.
>>
>> Just go back to the definition in section 4.3.1 of the manual.
>> Interactions are additive, so the formula holds true for the 
>> individual
>> dispersion and repulsion parts of the Lennard-Jones potential.
>>
>> Cheers,
>>
>> Erik
>>
>>
>>
>> On Monday, October 6, 2003, at 01:11 PM, Ilya Chorny wrote:
>>
>>> I don't understand. I'm am only interested in what happens to the
>>> softcore distortion if C6 = 0. In  this case is sigma^6 = sc_sigma^6.
>>>
>>> Thanks
>>>
>>> Ilya
>>>
>>>
>>>
>>> On Mon, 2003-10-06 at 12:48, Erik Lindahl wrote:
>>>> Hi,
>>>>
>>>> The softcore sigma value is used for the softcore distortion/scaling
>>>> of
>>>> the potential, not the actual interaction.
>>>>
>>>> If both c6 & c12 are positive, it is calculated from sigma^6=c12/c6,
>>>> otherwise the default value is used.
>>>>
>>>>
>>>> Hence, If you have c6=0 for a particular interaction, the dispersion
>>>> part will be zero no matter what the sc_sigma value is.
>>>>
>>>> Cheers,
>>>>
>>>> Erik
>>>>
>>>>
>>>> On Monday, October 6, 2003, at 12:14 PM, Ilya Chorny wrote:
>>>>
>>>>> Hi I was wondering if anybody has an answer to my question?
>>>>>
>>>>> Ilya
>>>>>
>>>>> On Thu, 2003-10-02 at 10:11, Ilya Chorny wrote:
>>>>>> Hello
>>>>>>
>>>>>> In the manual it says that by default sc_sigma = .3 nm.
>>>>>> What C6 value does this correspond to. More specifically I have C6
>>>>>> set
>>>>>> to 0.0. What will gromacs use as the C6 value in the soft core
>>>>>> potential.
>>>>>>
>>>>>> Thanks
>>>>>>
>>>>>> Ilya
>>>>>
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