[gmx-users] C6 attractive term off OPLSAA

nishap.patel at utoronto.ca nishap.patel at utoronto.ca
Tue Nov 30 17:52:46 CET 2010

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



-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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