[gmx-users] C6 attractive term off OPLSAA

[nishap.patel at utoronto.ca]

Okay I am going to give it a try. I just wanted to make sure I was  
calculating C6 and C12 correctly as well using sigma and epsilon  
according to rule 3

C12 = Sigma^(6)*C6
C6 = 4*sigma^(6)*epsilon

Thanks


Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:

>
>
> nishap.patel at utoronto.ca wrote:
>> Hello,
>>
>>   I have a concern regarding C6 attractive term in LJ potential. I   
>> am using OPLS-AA force field, and I wish to turn off attractive   
>> term C6 by setting the parameters to zero. One of the suggestion   
>> was to add a [nonbond_params] in my ffoplsaanb.itp file and set the  
>>  C6 to zero between the non-bonded pair. In my system for example,   
>> which consists of one methanol in water, I wish to set C6 term to   
>> zero between my solute and solvent. Since OPLSAA is all atom force   
>> field it treats each atom individually and has sigma and epsilon   
>> for each atom, so I am not sure how I would actually set my   
>> nonbond_params in my nb.itp file. I realize I need to convert each   
>> sigma and epsilon to C6 and C12, so say for example for methanol in  
>>  water my [nonbond_params] would look something like this?
>>
>> [ nonbond_params ]
>> ; i    j func          c6           c12
>>      CT        OW  1   0.00      calculated value for C12 here?
>>      CT        HW1  1  0.00
>>      CT        HW2  1  0.00
>>
>> CT is the carbon in Methanol. OW, HW1 an HW2 correspond to atoms in  
>>  TIP3P water model
>>
>> Is that correct? Would I have to do that for each atom in methanol?
>>
>
> Sounds about right to me.
>
> -Justin
>
>> Any suggestions would be appreciated.
>>
>> Thanks.
>>
>> Nisha P
>>
>
> -- 
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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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