[gmx-users] g_rmsf -res
carlajamous at gmail.com
Fri Jun 11 11:08:33 CEST 2010
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
On Fri, Jun 11, 2010 at 10:53 AM, Erik Marklund <erikm at xray.bmc.uu.se>wrote:
> 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).
> 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?
>> 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).
>> 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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