[gmx-users] Root-mean-square deviation

[Ran Friedman]

Just use the -res flag.

Ran.

Gia Maisuradze wrote:

> 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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>
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-- 
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Ran Friedman
Laser Laboratory for Fast Reactions in Biology
Department of Biochemistry
Faculty of Life Sciences
Tel-Aviv University
Tel. +972-3-6409824
Fax. +972-3-6409875
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