[gmx-users] distance constraints

Michal Kolinski mkolin at iimcb.gov.pl
Tue Feb 21 12:18:51 CET 2006

Mark advice helped me to solve my problem, 
now it works fine just the way I wanted. 
Manual says "For constraints between 
molecules the pull code can be used." and I 
wanted to know is there a simple way to do this.  
Mark thank you for script, it works fine.

Uwe Richter wrote:
> Hi Mark,
> I assume Michal knows how to define distance restraints. That's described
> in the manual. 

It would be good to be able to assume that :-) Unfortunately my 
impression is that many people who post haven't done enough work 
themselves on the problem... to the point that they haven't read the 
manual (well enough). One could certainly interpret Michal's question in 
the way you did, though!

 > The problem is you can't do this between different
> 'molecules',
> as you know. I think 'molecule' might not be the best expression in this 
> context.

Indeed, I carefully used the word 'topologies' - probably not perfect 
given the specific GROMACS usage, but something like 'assemblies' or 
'systems' aren't quite right either... 'structures'?

> You can very well have many molecules in one topology section, which has 
> the
> advantage that it is possible to define distance restraints between 
> them. Of
> course this setup also has its disadvantages. It really depends on the 
> project.

That you have to merge the topologies to be able to have the option of 
restraints is a good point - one I hadn't encountered before. Thanks.

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