[gmx-developers] New constraint algorithm based on SHAKE: Some doubts

Lorién López Villellas lorien.lopez at bsc.es
Tue Jun 1 16:27:39 CEST 2021

Hello, all.

We are working on a new constraint algorithm based on SHAKE. We already
have two versions working in GROMACS; a serial one that works with any kind
of molecule, and a parallel one that only works with peptide chains. The
results we have obtained so far are very promising.

We are trying to extend the algorithm to also work in energy-minimization
runs. However, we have seen that SHAKE is not supported in this kind of
runs, is there any reason behind that?

One of the following steps is to support MPI. Currently, our parallel
version only works with OpenMP on a single node. In order to work in
parallel, we use a precise bond numbering that allows us to distribute the
constraints between the threads in a very particular manner. This gives us
a very good performance, but it makes it difficult to support MPI with the
current domain decomposition implementation, in which two atoms of the same
molecule can be in different ranks. As far as we know, there is an option
to prevent constraints of the same molecule from being in different ranks
(update groups). However, we are guessing it is not a good idea to rely on
that option, right? Another alternative would be to send all of the
required information (the positions mainly) of a molecule in each time-step
to a single node to execute the algorithm. We are open to any suggestion or
idea you can provide.

Thank you very much in advance,


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