[gmx-users] Non bonded parameters
jalemkul at vt.edu
Thu Dec 28 23:07:36 CET 2017
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].
> 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 A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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