[gmx-users] Regarding g_cluster process MPI enabled

francesco oteri francesco.oteri at gmail.com
Tue Oct 2 15:45:36 CEST 2012

you have to implement the algorithm using parallel paradigma (MPI, openmp,
Alternatively, there is a workaround to bypass the serial rmsd matrix
building (the most
time consuming part).
g_cluster reads a rmsd matrix as input, you can run different rmsd instance
in parallel,
using appropriate input, in order to obtain the different rows of the
Next, you have to collect these outputs through in order to have the .xpm
file through an
appropriate script (that you have to write).
This matrix can be used as input to g_cluster that will use it to calculate


2012/10/2 R.Vidya Rajendran (10PHD013) <vidya2010 at vit.ac.in>

> Dear Friends,
> Gromacs script such as g_cluster takes lot of time to complete in a
> single machine. Is their any way to give this job to a cluster machine
> like mdrun. Since mdrun is MPI enabled so I can easily execute it on
> cluster.
> Anybody in group have any clue that how we can execute g_cluster
> command on a cluster machine ?
> regards
> Vidya
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Cordiali saluti, Dr.Oteri Francesco

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