[gmx-users] constraint pull code / gromacs 5.0.4

[Alex]

>
>
> It's dangerous to make broad generalizations like "constraints should be
> deprecated."  Sometimes constraints are not appropriate (materials,
> crystals, etc).  But for the vast majority of biomolecular simulations, we
> really don't care about different vibrational states of bonds involving H,
> so there's zero purpose to running our simulations 4x slower just to
> collect information we don't need :)
>
>
> Here he is. :) My not entirely serious comment aside (and not to hijack
the thread), how is the analytical calculation of forces in harmonic
springs computationally heavier than something like SHAKE or LINCS? Are you
guys doing something algorithmically superfancy with LINCS? I recall
implementing both SHAKE and LINCS and for the life of me can't see where
the x4 factor comes from.