[gmx-developers] soft-core atom selection

Berk Hess hess at kth.se
Wed Nov 19 09:36:32 CET 2014


Soft-core is not decided on an atom basis. A pair interaction is 
soft-cored when at least one of the two atoms is perturbed and at least 
one of the atoms has c12=0 at lambda=0 or lambda=1. So for atoms with 
LJ, interactions are only soft-cored when strictly necessary. For atoms 
without LJ, e.g. many hydrogens in many force fields, all perturbed 
interactions are soft-cored. For such atoms soft-coring is necessary 
when connected to a heavy atom that is decoupled. So the only cases 
where some interactions are soft-cored that are not strictly necessary 
is in a system where some atoms are decoupled and others are modified, 
then interactions with hydrogens connected to modified atoms would not 
need to be soft-cored.



On 11/18/2014 11:45 PM, David Mobley wrote:
> Hi,
> 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 parameters?
> Thanks!
> David

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