[gmx-users] constrain atoms at the moving sites

[Mark Abraham]

Xinghua Shi wrote:
> Hi gmx users,
> 
> Does anybody know how to constrain some atoms at the positions which
> are not fixed during MD simulation? That's mean, the atoms are
> constrained with some other molecules, instead of being fixed at the
> coordinate sites.
> I know the pull code can do such things by using the function
> CONSTRAINT. Yet the problem is that in this code we have only one
> reference group. If I have many atoms to be constrained at different
> reference sites, how can I do?

Look in the manual for "restraints"

Mark