[gmx-users] Root-mean-square deviation

[Gia Maisuradze]

Ran,

Thanks. It works now.

Gia

----- Original Message ----- 
From: "Ran Friedman" <ran at hemi.tau.ac.il>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Wednesday, May 18, 2005 6:44 AM
Subject: Re: [gmx-users] Root-mean-square deviation


> 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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> 
> 
> -- 
> ------------------------------------------------------
> 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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