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

Andras Szilagyi sziami at gmail.com
Thu Jul 2 17:23:04 CEST 2015


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?


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