[gmx-users] the 2 nd column of the output of g_cluster with -dist option

[Xavier Periole]

On Wed, 13 Feb 2008 00:46:33 +0200
  "OZGE ENGIN" <OZENGIN at KU.EDU.TR> 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" <X.Periole at rug.nl>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> 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" <OZENGIN at KU.EDU.TR> 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
-----------------------------------------------------