[gmx-users] Root-mean-square deviation

[Gia Maisuradze]

Hi,

In my previouis email my question was about rmsd as a function of residue 
number. Later I found the same kind of question in archive, and the answer 
was g_rmsf program. I have tried this program and got rmsd as a function of 
atom number. I was trying to get an index file with all residues listed 
there, but g_rmsf still gives rmsd dependence on atom number. Perhaps I am 
not doing index file correctly. How can I create the index file with all 
residues listed? Could anyone help me with that?

Thanks.

Gia Maisuradze


----- Original Message ----- 
From: "Gia Maisuradze" <gia at chem.unr.edu>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Tuesday, May 17, 2005 10:27 AM
Subject: Re: [gmx-users] Root-mean-square deviation


> Hi,
>
> I am studying the dynamics of different mutants of lambda repressor. I 
> would like to calculate rmsd as a function of residue number. Gromacs has 
> a few different programs to calculate rmsd dependence on time, but I could 
> not find the dependence on residue number.
>
> Is there any program in Gromacs which can perform this kind of 
> calculation?
>
> Thanks.
>
> Gia Maisuradze
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