[gmx-developers] ensemble code and restraints

Robert Fenwick robert.fenwick at irbbarcelona.org
Tue Dec 9 11:50:52 CET 2008

Hey Mark thanks for that, it does seem that this is a similar case.


2008/12/9 Mark Abraham <Mark.Abraham at anu.edu.au>:
> Robert Fenwick wrote:
>> 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.
> There are some implementation similarities between what you propose and
> REMD. (I think) that at each(?) MD step you will need to swap certain atomic
> positions between pairs of simulations so that each simulation master
> process can then apply the pair-averaged restraint force without further
> inter-simulation communication. In REMD, at every so many MD steps, you swap
> the potential energy of certain pairs of simulations, and then maybe the
> whole simulation state. You can get a fair idea of how you should approach
> this project by understanding the REMD algorithm.
> Probably your most efficient implementation is to use some nonblocking MPI
> sends and receives for the relevant subset of positions before you start
> doing the normal nonbonded kernel loops, so that the communication completes
> by the time you're done with the kernels and are ready to add in the
> restraint forces. I've no idea how well that approach suits modifying the
> existing implementation of intra-simulation restraints.
> Mark
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