[gmx-users] C6 attractive term off OPLSAA

Justin A. Lemkul jalemkul at vt.edu
Wed Dec 1 16:25:02 CET 2010 


nishap.patel at utoronto.ca wrote:
> I ran the simulation using a different force field ffG53a6. I modified 
> the ffG53a6nb.itp file by changing the term C6 to zero for nonbonded 
> parameters, but this time for urea in water. The simulation ran fine 
> without any warning or exploding. I don't understand why it would work 
> with one force-field and not with OPLS-AA.
> 

I don't understand why it worked at all, frankly, but more than likely you've 
been lucky enough to make 53a6 work, but OPLS-AA failed.  You're making 
significant alterations to the nonbonded interactions of the system.

> Also using mdrun -rerun, I would basically use the nb.itp file with 
> nonbonded parameters as mentioned earlier and everything else is the 
> same i.e. my .mdp parameters and do another run using my previous 
> trajectory file? I tried to look through some of the posts for using 
> -rerun but I don't understand how that would not still blow up the 
> system. I would like to give it a try for sure but I am not quite sure 
> how I would use the command as such.
> 

Using mdrun -rerun recalculates energies from an existing trajectory.  You would 
generate a trajectory with a normal force field model, then create a new .tpr 
file that has your modified potential, such that you can decompose the energy 
terms cleverly.  If your goal is to generate trajectories to study the effects 
of using a modified potential (i.e., C6 = 0), then you can't use -rerun.

-Justin

> I really appreciate the help.
> 
> Thanks.
> 
> 
> Quoting Mark Abraham <Mark.Abraham at anu.edu.au>:
> 
>> 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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>>>
>>
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> 
> 
> 

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

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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