[gmx-developers] soft-core atom selection

David Mobley dmobley at gmail.com
Tue Nov 18 23:45:56 CET 2014


I wanted to ask concerning soft-core potentials in GROMACS: How is it
determined which atoms are soft core? Specifically, some other code bases
allow the option to select specific atoms which are going to be treated
with LJ soft core potentials, while other atoms are not treated in this way
and maintain their normal potential or a linear mix of their A and B state
potentials. In GROMACS, there is no option to select this that I am aware
of, so I'm assuming that soft core is applied to all atoms, or to all atoms
which have different A and B states or different A and B state LJ

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