[gmx-users] g_rmsf

Justin A. Lemkul jalemkul at vt.edu
Mon Jul 28 23:20:39 CEST 2008

sudheer babu wrote:
> Hi,
>     I would like to calculate B-factor of protein, so I performed 
> command like this
> g_rmsf  -f  .xtc  -s  .tpr   -res  -o  fluctuate.xvg -od devi.xvg it has 
> run without error.Now i am bit doubting that which .xvg file  have to 
> take for plot B-factor values?

I think you have not specified the correct options.  Check g_rmsf -h and read 
about the -oq option.


> B-factor is nothing but thermal devation of atoms. I think, I should 
> take dev.xvg for plotting B-factor values, if it is coorect, then what' 
> s the need for  producing  fluctuate.xvg? may be this is trivial question.
> Could anyone help me pls.
> Thanks alot in advance
> ------------------------------------------------------------------------
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list