Hi Efrat, 2011/5/3 Efrat Noy <[email protected]>: > Hi, > > I have 2 questions regarding root mean square fluctuation calculations: > > 1. what exactly is the difference between the values in the rmsf.xvg file > and the values in the rmsdev.xvg file (obtained with the -od option)? Are > the rmsf.xvg values are standard deviations of atom positions along the > trajectory with respect to an average structure of the trajectory? And > rmsdev.xvg values are the same but in respect to a reference structure > defined by the tpr file?
The help is pretty clear on the first part: -od gives the RMSD w.r.t. the reference. You're right on the nature of the RMSF. > > 2. Is it possible to fit the trajectory structures, prior to rmsf > calculations, on only part of the protein? Yes. You can preprocess the trajectory with trjconv and use the -nofit option to g_rmsf. Cheers, Tsjerk > Thanks, Efrat > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
