[gmx-developers] ensemble code and restraints

Robert Fenwick robert.fenwick at irbbarcelona.org
Tue Dec 9 10:58:37 CET 2008

Hi Berk,

It has been shown a few times now that averaging over a single
structure is not sensible as it is possible to get strained
structures, the other alternative is to do as you suggest to average
over the whole ensemble. This also creates problems and if you average
over three or more structures then it is possible that one completely
unfolds while the others compensate. The same work has shown that if
you average over pairs of structures you get around this problem. In
theory I can do all of this in CHARMM. What I would like to know is
how to implement a similar scheme in GROMACS, so that others can use
it. I am currently lost in the source code and was looking for some
pointers as to how I could get started.

Thanks for all the help and suggestions,


2008/12/9 Berk Hess <hessb at mpip-mainz.mpg.de>:
> Hi,
> I don't understand why you want to ensemble restrain only over pairs
> (and I don't have time to read papers).
> Ensemble restraining mimics real NMR experiments where
> you have a large number of molecules in a test tube and
> you measure an ensemble averaged signal.
> Such signals are r^-6 averaged over all pairs.
> Because of the extremely non-linear averaging, if one pair
> out of 10 is a bit below the upper bound, there will be no
> force on all 10 pairs.
> Berk
> Robert Fenwick wrote:
>> OK I am still a bit lost about the restraining of distance restraints
>> over pairs of structures within an ensemble. I have looked at the
>> manual and it seems that what I would like to do is indeed ensemble
>> averaging over pairs. How is it possible to specify which replicas are
>> involved? I essentially want to treat these pairs as dimers, so that
>> there is only a force on the molecules if both structures in a pair do
>> not fulfill a distance restraint.
>> The system suggested by Richter et al. is a chain loop, i.e. pairs of;
>> 1 and 2, 2 and 3, 3 and 4, 4 and 1
>> Cheers,
>> Bryn
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