VMD-L Mailing List

From: pbrenne1_at_nd.edu
Date: Sun Jan 09 2005 - 13:25:16 CST

Axel, Luis, and Adrian,

Thank you for the replies. I will look into the cluster analysis implemented in
Gromacs. I did not see source available for the NMRcluster program and I prefer
to work with open source software. VMD ( & tcl) provides all of the RMSD data I
need in a convient output text file which I can then process in a small C++
application. I have yet to be convinced to join the world of Python users
opting for "traditional" scripting via bash and application coding in C++ (or
occasionally Java). Utilization of VMD has only recently introduced me to the
world of tcl.

Thanks again for your responses,
Paul Brenner

Quoting Axel Kohlmeyer <axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de>:

>
> >>> "PB" == pbrenne1 <pbrenne1_at_nd.edu> writes:
>
> PB> Hello,
>
> hello paul,
>
> PB> Does anyone know if there is a built-in or plugin module for VMD to do
> cluster
> PB> analysis over a set of dcds? I have used VMD in the past to calculate
> RMSDs,
> PB> but currently I would like to perform conformational cluster analysis as
> PB> referenced by Smith, Daura, and Gunsteren in their 2002 Proteins paper.
> The
> PB> analysis is not difficult but a matrix (vector of vectors etc...) would
> be nice
> PB> to store the RMSD values in. From the VMD manual I understand that tcl
> is not
> PB> well suited for mathematical operations such as these. I have also
> noticed the
>
> it depends on how much mathematics you need. e.g. we have a package for
> principal component analysis here, which is currently done completely
> in tcl and to make it work reasonably fast for larger systems, we
> hope to be able to get away with supplying one(!) lapack call
> via an additional binary plugin. also for other analysis tools we have
> found, that is is usually sufficient to implement only the key routines
> as binary plugins and then do the rest with scripting. writing all
> the 'glue-code' is _much_ faster in a scripted language.
>
> alternatively, you can try using the python interface, which should
> be much faster for computations.
>
> PB> Cluster visualization plugin contributed by researchers at Cornell but my
> PB> initial review found that it required the actual computation be done via
> a
> PB> program written by the Sutcliffe Group in 1996 which does not appear to
> be open
> PB> source.
>
> there is a freely available cluster analysis tool in the gromacs package:
> http://www.gromacs.org/documentation/reference_3.2/online/g_cluster.html
>
> the only thing you'd need now is to convert your trajectories to
> a format readable by gromacs. incidently, i have just hacked writing
> support into the gromacs/trr-plugin for exactly the same reason. ;-)
>
> i'll send in a patch soon, so that the next version of VMD should
> have that included. please get back to me, if you want it now.
>
> best regards,
> axel.
>
> PB> Thanks for any responses and my compliments on the VMD framework,
> PB> Paul Brenner
>
> --
> =======================================================================
> Axel Kohlmeyer e-mail: axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de
> Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673
> Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045
> D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
>