[gmx-users] Dummy atoms flopping everywhere

[Alessandra Villa]

Hi,

On Mon, Nov 25, 2019 at 6:20 PM Raphaël Robidas <raphaelrobidas at gmail.com>
wrote:

> I am doing a free energy perturbation calculation on a protein-ligand
> system. I am going from a topology A which has a benzyloxy group to a
> topology B which only has a methoxy group. My problem is that when lambda =
> 1, the simulation crashes because the benzyloxy group is flopping around
> too fast, since it has no mass nor collision. I am wondering that the best
> way to deal with this would be.
>
>
If  you switch off only the non-bonded interactions when going from A to B,
this should not happen since  the bond interactions (e.i. torsion) are
still active for the benzyloxy group (thus the benzyloxy group can not
freely rotate).
Best regards
Alessandra


> Using restraints would be an option, but I don't need to restrain my ligand
> otherwise, so it would be desirable to avoid restraints overall. Could a
> second topology without the dummy atoms be used just when lambda = 1 or it
> won't be compatible with the rest of the simulations?
>
> Thank you!
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>