[gmx-users] Constraining two virtual sites

[Sebastian Fritsch]

Hi again,


unfortunately I would need the constraint for a large number of molecules, say ~1000 i.e. 2000 vsites representing a few atoms each.
The constraint length should however be the same for each molecule. 

Assigning groups for each constraint group would not be possible due to the group limit I guess.
The do_constraint function in pull.c does not look too complicated, do you think it would be reasonable to adapt it a bit and call it
from some function like calc_bonds which comes after vsite construct and before vsite spread? The constraint forces in my case should be
be completely determined by the vsites, or am I wrong? Is there an easier solution?


Thank you,
Sebastian

> Hi,
>
> Unfortunately constraints can not be applied to virtual sites and grompp apparently
> does not not check for this. I will add a check.
> Constraints between virtual sites can lead to very complex constraint equations
> between the masses involved. Thus the general case if difficult to implement.
> Your cases seems quite simple and could be done with the pull code,
> if it would support more than one reference group, which I was thinking to implement.
>
> How many molecules do you have?
>
> Berk
>