[gmx-users] dummies and positional restraints

Frauke Meyer fmeyer at iris3.simm.ac.cn
Wed Aug 25 02:16:02 CEST 2004

Hi Berk,

> >
> >
> >But it does not. I tested by running two simulations that only differ
> >in that the ligand consists of normal atoms in one and of dummy atoms in
> >the other one (atoms just differ in charge and LJ parameters).
> >The dummy ligand moves, the 'normal' ligand does not.
> There is no difference in free-energy no/yes and lambda
> between the two simulations?

No difference, I am running just usual MD, free_energy = no

> Because the position restraint force constants for topology B
> might be zero. grompp will warn about this.
> In that case you would need to add 1000 1000 1000
> to each position restraint.

Right, with free_energy = yes and dummies in the topology I get 
this warning. But still, in the usual MD, why do the posres not work for

> Berk.
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