I looked at g_rmsf -h but the problem is that it's not clear enough. The help doesn't state how g_rmsf works & what does it calculate exactly. Because the definition of an RMSF is the following: "the mean-square fluctuation is a measure of the deviation between the position of particle i and some reference position. Typically, this reference position will be the time-averaged position of the same particle i." So does g_rmsf calculate the average structure & then the RMSF according to this average structure? Or does it calculate the RMSF after fitting to a reference structure that I would have specified with the option -s?
Thanks Carla On Tue, Feb 16, 2010 at 3:54 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > On 17/02/10 01:12, Carla Jamous wrote: > >> Hi everyone, >> please I need to calculate RMSF after fitting to the average structure >> of my MD simulation. >> Can anyone tell me how to do that? (especially, how to calculate the >> average structure) >> > > g_rmsf. There's a section in the manual that gives a breakdown of the > GROMACS tools by topic that can help guide you. > > > Another question that may sound stupid: does the "-s" have the same >> function with trjconv & g_rmsf? Can anyone clarify this option for me? >> > > Use the -h flag to the tool to see a description of how things work. > > Mark > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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