[gmx-users] g_rmsf -res

[Carla Jamous]

Please does anyone know how is calculated the B factor in gromacs? What is
the formula that gives the B factor with the average coordinates with
g_rmsf?

Carla

On Fri, Jun 11, 2010 at 10:53 AM, Erik Marklund <erikm at xray.bmc.uu.se>wrote:

> Hi,
>
> yes it can be done with g_covar, but such an average structure is often of
> little physical significace. Imagine for instance the acerage structure of a
> rotating methyle group (it's a bunch of atoms on a line).
>
> Erik
>
> Carla Jamous skrev:
>
>> Hi Tsjerk,
>>
>> thank you for your answer.
>> Actually, for the initial structure, I took the values of the B factor,
>> and calculated the mean square displacement per atom. This is what I meant
>> by saying RMSF of initial structure. Anyway, thanks for the explanation.
>>
>> But I have another question: I need to take 3 structures and make an
>> average structure of these 3. Is there a way to do it with gromacs?
>>
>> Cheers,
>> Carla
>>
>>
>> On Thu, Jun 10, 2010 at 12:15 PM, Tsjerk Wassenaar <tsjerkw at gmail.com<mailto:
>> tsjerkw at gmail.com>> wrote:
>>
>>    Hi Carla,
>>
>>    On Thu, Jun 10, 2010 at 12:03 PM, Carla Jamous
>>    <carlajamous at gmail.com <mailto:carlajamous at gmail.com>> wrote:
>>    > Hi Everyone,
>>    >
>>    > please I have a question concerning g_rmsf.
>>    > I need to compare the RMSF from my initial structure to the RMSF
>>    of my
>>    > average structure.
>>
>>    Single structures (initial c.q. average) do not have an RMSF.
>>
>>    > When I did
>>    >
>>    > g_rmsf -s .tpr -f .xtc -n .ndx -b xx -e yy -o rmsf
>>    >
>>    > or
>>    >
>>    > g_rmsf -s .tpr -f .xtc -n .ndx -b xx -e yy  -res -o rmsf
>>
>>    This is not what you did. Please copy/paste command lines.
>>
>>    > I got the same result, when choosing C-alpha for root mean square
>>    > calculation.
>>
>>    Sure, when selecting C-alphas, averaging the RMSF per residue
>>    (sum_over_calphas_in_residue/number_of_calphas_in_residue) will
>>    evidently be identical to calculating the RMSF on an atom basis for
>>    each Calpha.
>>
>>    > So please can anyone explain how can I get the average per
>>    residue over a
>>    > period of time?
>>
>>    Select 'protein' (and use the -res flag).
>>
>>    Cheers,
>>
>>    Tsjerk
>>
>>
>>    --
>>    Tsjerk A. Wassenaar, Ph.D.
>>
>>    post-doctoral researcher
>>    Molecular Dynamics Group
>>    Groningen Institute for Biomolecular Research and Biotechnology
>>    University of Groningen
>>    The Netherlands
>>    --
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>>
>
> --
> -----------------------------------------------
> Erik Marklund, PhD student
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
> phone:    +46 18 471 4537        fax: +46 18 511 755
> erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/
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