[gmx-users] C6 attractive term off OPLSAA

[Justin A. Lemkul]

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.

-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
>>>
>>> ========================================
>>> -- 
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> Please don't post (un)subscribe requests to the list. Use the www
>>> interface or send it to gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> 
> 

-- 
========================================

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

========================================