On Wed, 13 Feb 2008 00:46:33 +0200
"OZGE ENGIN" <[EMAIL PROTECTED]> wrote:
Xavier,
The output file of g_cluster with -dist option then gives the histogram of
rmsd value distribution, is it?
yes
If it is the case, after plotting these data,I observe that the distribution
resembles a gaussian type, its mean is located around 0.4 nm. This value is
bigger compared to yours. Is it feasible?
I performed my remd simulation in vacuum. It may be the reason?
Considering that it is REMD in vaccum, it looks like it should, the
protein unfolds and has an average rmsd of 0.4 nm. Nothing surprising.
I think you had different comments on this type of simulations ...
-----Original Message-----
From: "Xavier Periole" <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users <[email protected]>
Date: Tue, 12 Feb 2008 23:10:02 +0100
Subject: Re: [gmx-users] the 2 nd column of the output of g_cluster with
-dist option
On Tue, 12 Feb 2008 23:55:35 +0200
"OZGE ENGIN" <[EMAIL PROTECTED]> wrote:
Hi all,
What does the second column of the output file of g_cluster with -dist
option stand for? Its title is a.u. I think it is atomic unit? In the manual,
it is not described.
I believe a.u. stands for arbitrary unit. It should be the normalized
distribution. You can check by integrating the curve ... should be one.
XAvier
Thanks in advance
Ozge Engin
=================================
Computational Science & Engineering
Koc University
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-----------------------------------------------------
XAvier Periole - PhD
NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------
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Ozge Engin
=================================
Computational Science & Engineering
Koc University
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-----------------------------------------------------
XAvier Periole - PhD
NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------
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