[gmx-users] Non bonded parameters

[Anjana Jayasinghe]

 Dear gmx users,
Thank you very much for the reply. Appreciate, if you could further explain " remove any instance of that particular type from [nonbond_params] unless additional off-diagonal terms are required". 



    On Friday, 29 December 2017, 8:44:55 am AEDT, Justin Lemkul <jalemkul at vt.edu> wrote:  
 
 

On 12/28/17 4:24 PM, Anjana Jayasinghe wrote:
> Dear All,
> If I change (I want to use non-boned parameters defined in a published article) the single atom Lennard-Jones interactions parameters (C6 and C12 present in [atomtypes] of ffnonbonded.itp) do I need to change C6 and C12 present in [nonbond_params] section ?
> Could you please anyone help me?

The parameters set in [atomtypes] apply to all LJ interactions computed 
via normal combination rules. The [nonbond_params] directive specifies 
values that override combination rules. If you want to apply a global 
change to C6/C12, then you should change what is in [atomtypes] and 
remove any instance of that particular type from [nonbond_params] unless 
additional off-diagonal terms are required.

-Justin

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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry

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