[gmx-users] Verlet cutoff scheme and implicit solvent with PBC=no

Mark Abraham mark.j.abraham at gmail.com
Thu Jul 2 17:29:08 CEST 2015


That is indeed a current limitation. There's plans to make infinite cutoffs
possible before we remove the group scheme. Not sure if there is draft code

The implicit solvation code, even in the group scheme has had essentially
no testing since 4.6 (e.g. search the archives for other such threads), so
I might only trust it running in a single thread. GROMACS 4.5.7 is probably
your best choice.


On Thu, Jul 2, 2015 at 5:23 PM Andras Szilagyi <sziami at gmail.com> wrote:

> Hi,
> I've tried to set up implicit solvent simulations in Gromacs 5.0.2. It
> is recommended that one uses PBC=no and infinite cutoffs for implicit
> solvent (GBSA) simulations. However, if I use the Verlet cutoff
> scheme, grompp throws an error, saying that Verlet doesn't support
> PBC=no. If I use group as cutoff scheme, grompp informs me that this
> is deprecated and will be removed in future releases. So, in the
> future, PBC=no and infinite cutoffs will be impossible? Implicit
> solvent simulations will have to be done with periodic boundary
> conditions and finite cutoffs?
> Andras
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