[gmx-users] control parameter on the Lennard-Jones interactions

[battistia at libero.it]

Dear  Mark,

many thanks for your suggestions!

Indeed adding of  the [ pairtypes ] section seems to solve. Can I asky you which is the difference between [ paitypes ] and [ nonbond_params ] for intramolecular pair interactions? they look very similar:

[ pairtypes ]

; i   j func  V(c6) W(c12)

A  B  1  0.22617E-02  0.74158E-06

[ nonbond_params ]
; i   j func  V(c6) W(c12)

A  B  1  0.22617E-02  0.74158E-06

What is the difference?

Many thanks,

Anna

Nb.: for some kind of problem I do not know, I did not received your messagge, in my mail-box. I just saw it now from the gromacs.org_gmx-users Archives.  So, I cut and copy below your messagge in order to complite the topic for everyone.

>Hi,

> This should be possible, e.g. with [pairs] on those particular atoms, or perhaps with tabulated non-bonded interactions (unfortunately > only available with the group scheme)

> Mark


> Il 20 maggio 2019 alle 21.05 battistia at libero.it ha scritto:
> 
> 
>     maybe I can add  the following section in the itp file (only for the A and B atom) and then vary the W(c12) factor
> 
>     [ nonbond_params ]
>     ; i   j func  V(c6) W(c12)
> 
>     A  B  1  0.22617E-02  0.74158E-06
> 
> 
>     if this is ok, it is very simple!
> 
>     Can I define the func 1 for the atom A and B if for the system I used the func 2 (sigma and eps rather then C6 and C12)? I suppose I can, right?
> 
>     Thank you very much!
> 
>     Anna
> 
> 
>         > > Il 20 maggio 2019 alle 18.15 battistia at libero.it ha scritto:
> > 
> > 
> >         Dear all,
> > 
> > 
> >         by considering there is no response to my post, I suppose in gromacs there is no way to solve exactly my problem.
> > 
> >         Also if no exactly, has anyone a kind of suggestion to go in the direction of my calcultation?
> > 
> >         Many thanks in advance,
> > 
> >         Anna
> > 
> > 
> > 
> >             > > > Il 16 maggio 2019 alle 7.17 battistia at libero.it ha scritto:
> > > 
> > > 
> > > 
> > >             Dear gromacs members,
> > > 
> > >             I would ask you if in gromacs is possible to add a control parameter on the Lennard-Jones interactions.
> > >             For example we have two atoms A and B and the corresponding parameters;  sigma(A), eps(A),  sigma(B), esp(B); then for the A-B interactions we have the parameters obtained with the Lorentz-Berthelot or with the geometrical average.
> > > 
> > >             I would like to have a standard interaction between A or B with the other atoms of the system.  In the same time I would like to add a control parameter C on the interaction between A and B to have the following potential:
> > >             V(r(AB))=4*eps(AB)*[(sigma(AB)/r(AB))^(12)-C*(sigma(AB)/r(AB))^(6)]
> > > 
> > >             Is it possible? How can I manage this calculation?
> > > 
> > > 
> > >             Many thanks,
> > > 
> > > 
> > >             Anna
> > > 
> > > 
> > > 
> > > 
> > > 
> > >         > > 
> > 
> >          
> > 
> >     > 
> 
>      
>