[gmx-users] distance constraints
Mark.Abraham at anu.edu.au
Mon Feb 20 22:52:31 CET 2006
Uwe Richter wrote:
> Just define it as one molecule without any bonds, pairs,
> angles and dihedrals between the two entities.
> 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
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.
More information about the gromacs.org_gmx-users