[gmx-users] Non bonded parameters

[Justin Lemkul]

On 12/28/17 5:02 PM, Anjana Jayasinghe wrote:
>   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".

If you only need combination rule LJ values for that atom type, make 
sure it does not appear in [nonbond_params]. If you do need special 
combinations, make sure they are correctly listed in [nonbond_params].

-Justin

>
>
>      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
>

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

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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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