[gmx-users] C6 attractive term off OPLSAA

[Mark Abraham]

On 1/12/2010 5:06 AM, Justin A. Lemkul wrote:
>
>
> nishap.patel at utoronto.ca wrote:
>> I tried using the nonbonded parameters as defined below in my 
>> ffoplsaanb.itp file for methanol in water and this is the syntax I used:
>>
>> [nonbond_params    ]
>> ;i    j    func    c6    c12
>>   opls_154    opls_111    1    0.00E+000    2.43E-006
>>   opls_154    opls_112    1    0.00E+000    0.00E+000
>>   opls_154    opls_112  1    0.00E+000    0.00E+000
>>   opls_155    opls_111  1    0.00E+000    0.00E+000
>>   opls_155    opls_112  1    0.00E+000    0.00E+000
>>   opls_155    opls_112  1    0.00E+000    0.00E+000
>>   opls_156    opls_111  1    0.00E+000    2.70E-007
>>   opls_156    opls_112  1    0.00E+000    0.00E+000
>>   opls_156    opls_112    1    0.00E+000    0.00E+000
>>   opls_157    opls_111  1    0.00E+000    3.01E-006
>>   opls_157    opls_112  1    0.00E+000    0.00E+000
>>
>> When I tried to do mdrun, I got an error saying my system is 
>> exploding. I tried doing the mdrun without nonbonded parameters and 
>> it runs fine. So I am not sure if I am using the nonbond_params 
>> concept correctly. i.e. I want C6 to be zero between my solute 
>> (methanol) and solvent (water). This is the error:
>>
>> Warning: 1-4 interaction between 2 and 6 at distance 3.786 which is 
>> larger than the 1-4 table size 2.500 nm
>> These are ignored for the rest of the simulation
>> This usually means your system is exploding,
>> if not, you should increase table-extension in your mdp file
>> or with user tables increase the table size
>>
>> Suggestions?
>>
>
> Your implementation of your concept is technically correct, but 
> perhaps physically unreasonable.  You're turning off the attractive LJ 
> component and leaving only a repulsive component.  It sounds about 
> right that everything is flying apart.

Indeed. The way to do this is with mdrun -rerun on a trajectory 
generated with the normal version of the forcefield, as I think I said 
in another thread yesterday.

Mark

>
> -Justin
>
>> Thanks.
>>
>> -Nisha P
>>
>> Quoting 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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>>
>>
>