[gmx-users] distance constraints

Maik Goette mgoette at mpi-bpc.mpg.de
Mon Feb 27 18:35:16 CET 2006

We also had those "problems".
It would be a great advancement to modify GROMACS, as David mentioned.


Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/

David Mobley wrote:
> All,
> Since we're on this subject, I would just like to gripe about this
> requirement that, in order to apply restraints (distance, angle,
> dihedral) between atoms, the atoms must be in the same 'molecule'
> definition in a GROMACS topology file. It's rather inconvenient. For
> example, I ran some calculations where I found some ordered waters got
> stuck in a protein during MD. I wanted to compute the free energy of
> removing those ordered waters from within the protein, in order to
> figure out whether it *really* was favorable for them to be in the
> protein, or whether they were just "stuck" because I hadn't run long
> enough. Currently, there is no way to do this in GROMACS without (a)
> renaming the waters so they're no longer recognized as solvent, (b)
> listing the waters as part of the protein 'molecule' (i.e. at the end
> each of the sections in the molecule definition for the protein,
> adding the relevant water parameters), and (c) editing the coordinate
> file (.gro) to  place the waters in question consecutively after the
> protein. I now have scripts that do this, of course, but it's a big
> pain. And I think it probably wouldn't be too difficult to cook up
> cases where you want to apply restraints between things that you
> simply CAN'T DO with the current code.
> It seems to me that the source of the problem is that topology files
> don't necessarily have unique atom numbering; rather, the atom
> numbering only runs within the same molecule definition. Hence if I
> specify restraints between atoms 11 and 73, GROMACS requires that they
>  be within the same molecule definition, otherwise it wouldn't be able
> to sort out which atom corresponds to atom 11.
> Probably there is a straightforward work around. I can think of two
> possibilities off the top of my head:
> (1) Add an additional restraint option which allows use of absolute
> atom numbering (i.e., the numbering that shows up in the .gro file).
> There's no ambiguity here, since in the .gro file, all of the atoms
> have unique numbers.
> (2) Add an option to specify the molecule(s) in which the atoms to be
> restrained are. Again, numbering from the .gro file would probably
> have to be used.
> Anyway, just a suggestion.
> Thanks,
> David
> On 2/21/06, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
>>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
>>>as you know. I think 'molecule' might not be the best expression in this
>>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
>>>advantage that it is possible to define distance restraints between
>>>them. Of
>>>course this setup also has its disadvantages. It really depends on the
>>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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