[gmx-users] gromos analysis

[Nuno R. L. Ferreira]

Hi

How did you converted dcd to xtc? Using trio?
Spite I'm not answering your question :( , I once tryed to this convertion
of formats, and I never succeeded.

Best regards,
Nuno

P.S.  You say that some gmx tools went just fine. Did you compared for e.g.
the rmsd obtained by g_rms with the one obtained with the vmd extension rmsd
tool? This is a way in order to say that the convertion went fine.  Do you
have 1000 frames in your dcd? Did you used another clustering method in
g_cluster, other than gromos?

----- Original Message ----- 
From: "Wei Fu" <fuwei at adrik.bchs.uh.edu>
To: <gmx-users at gromacs.org>
Sent: Tuesday, November 02, 2004 11:07 PM
Subject: [gmx-users] gromos analysis


> Hi, all,
>
>     We converted the NAMD trajectory to gromacs format (from dcd to xtc
> file), then use g_cluster
> to analyze it, but it gives the imcomplete result in cluster.log as
> follows:
>
> Using gromos method for clustering
> Using RMSD cutoff 0.1 nm
> The RMSD ranges from 0.0701927 to 0.306038 nm
> Average RMSD is 0.204764
> Number of structures for matrix 1000
> Energy of the matrix is 76.4664 nm
>
> Found 83 clusters
>
> _______________________________________________________________________
> cl. | #st rmsd | middle rmsd | cluster members
>   1 |  22 .201 |      0 .099 |      0      0      0      0      0      0
> 0
>     |          |             |      0      0      0      0      0      0
> 0
>     |          |             |      0      0      0      0      0      0
> 0
>     |          |             |      0
>   2 |  22 .196 |      0 .100 |      0      0      0      0      0      0
> 0
>     |          |             |      0      0      0      0      0      0
> 0
>     |          |             |      0      0      0      0      0      0
> 0
>     |          |             |      0
>   3 |  22 .192 |      0 .099 |      0      0      0      0      0      0
> 0
>     |          |             |      0      0      0      0      0      0
> 0
>     |          |             |      0      0      0      0      0      0
> 0
>
> ... ...
> _______________________________________________________________________
>
>     I wonder why all cluster member is 0?
>
>     I also did the other analysis like rmsd, rmsf, and essential dynamics
> analysis, all these commands work well.
>
>     Has anybody have idea about it? Thanks in advance!
>
> Linda
>
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