Thank you Mark for your feedbacks.
There is one more point that is not clear to me for the output of g_cluster, In
the second column of the "cluster.log" of g_cluster, the same rmsd values are
indicated for different clusters. What does it mean? Although these clusters
have the same cut-off value, they are grouped in different clusters, Why?
Thank you.
-Original Message-
From: Mark Abraham <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users
Date: Sun, 17 Feb 2008 22:35:20 +1100
Subject: Re: [gmx-users] distance options for g_cluster
OZGE ENGIN wrote:
> Hi all,
>
> I am trying to understand what type of distance can be used with g_cluster?
>
> In the manual, it is written that RMS deviation after fitting or RMS
> deviation of atom-pair distances can be used to define the distance between
> structures in the first paragraph.
> However, in the "other options" part, two options are indicated for
> -dista option, which indicates the type of distance that will be used with
> g_cluster. They are RMSD of distances or RMS deviation. Consequently, the
> information in the "first paragraph" does not coincide with that given in the
> "other options" part for -dista option.
>
> Maybe I could not understand. Could anyone explain this in a clearer way,
> please?
I agree that it is not very clear what is meant in the documentation,
and I have wondered myself what it means. This is one of the reasons
that the source code is made available.
I had a quick look, and "-dista yes" looks like it implements the "RMS
deviation of atom-pair distances" quoted above. That is, it forms an
atom-pair distance matrix for each structure in the trajectory, and then
does an all-against-all root-mean-square comparison of those matrices to
generate the structure comparison matrix for clustering. You'd be well
advised to verify that yourself. It's all in src/tools/gmx_cluster.c
Mark
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is made available.
I had a quick look, and "-dista yes" looks like it implements the "RMS
deviation of atom-pair distances" quoted above. That is, it forms an
atom-pair distance matrix for each structure in the trajectory, and then
does an all-against-all root-mean-square comparison of those
Ozge Engin
=
Computational Science & Engineering
Koc University
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