[gmx-users] Define intermolecular interactions in L-J simulation

[Li, Shi]

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> Den 2019-10-23 kl. 18:22, skrev Li, Shi:
> > Dear GMX users,
> >
> > I am wondering if there is a way to define the intermolecular interaction
> > to simulation a binary LJ system. For example, I have two atoms A and B,
> > they share the same LJ parameter, and I want to change the interaction
> > parameter between A and B, so that I would expect different behaviors
> from
> > the simulation (mix or phase separation).
> >
> > I checked the manual and found this can be defined in the topology file
> as
> > [intermolecular_interactions] and use the [pairs] interaction then list
> the
> > atom pairs. But it is still confusing if I have a system containing 500 A
> > and 500 B, how can I apply this to the entire binary system. I was
> > assumed that I can use atomtype instead of atom number? But how and where
> > to specify that?
> >
> > Any suggestions?
> >
> > Thanks,
> > Shi
> >
> Use
> [ nonbonded_types ]
> A A 1  c6 c12
> B B 1  c6 c12
> A B 1  c6 c12
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Head of Department, Cell & Molecular Biology, Uppsala University.
> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> http://www.icm.uu.se
>
>
> Thank you so much! This works very well.

Shi




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