[gmx-users] distance constraints

Uwe Richter urichter at jerini.de
Tue Feb 21 09:43:46 CET 2006

Hi Mark,

I assume Michal knows how to define distance restraints. That's described
in the manual. The problem is you can't do this between different 
as you know. I think 'molecule' might not be the best expression in this 
You can very well have many molecules in one topology section, which has 
advantage that it is possible to define distance restraints between them. Of
course this setup also has its disadvantages. It really depends on the 


Mark Abraham wrote:

> 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
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