[gmx-users] distance constraints

[Mark Abraham]

Uwe Richter wrote:
> Just define it as one molecule without any bonds, pairs,
> angles and dihedrals between the two entities.
> 
> Uwe
> 
> Michal Kolinski wrote:
> 
>> Hi all
>> Is it there a way to constraint distance between two
>> atoms of two separate molecules in gromacs?  Please give me some 
>> advice. Thank you
>> Michal.

Just merging the topologies won't constrain any distances... for a start 
you've not specified how strong the constraint interaction is. Further 
this would imply that all atoms in a topology were magically constrained 
somehow, because the algorithms don't know that these were originally 
two molecules that have been clerically combined - if distance 
constraints were introduced magically for your case, then the algorithms 
would be doing that all the time... and obviously they don't.

There's a section in the manual that goes into some detail about the 
sort of distance restraints it appears you want. Please have a read of it.

Mark