[gmx-users] Average structure & "-s"

Mark Abraham Mark.Abraham at anu.edu.au
Tue Feb 16 17:00:36 CET 2010

On 17/02/10 02:38, Carla Jamous wrote:
> 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?

 From g_rmsf -h:
"g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard
deviation) of atomic positions after (optionally) fitting to a reference

So it will do what you want. Apparently the fitting is optional. Further 
down you can see that the -s file is not optional, so presumably the 
program will prompt you about whether or not you want fitting to the -s 
structure. Try it and see.

> Or does it calculate the RMSF after fitting to a reference structure
> that I would have specified with the option -s?

The usual procedure is to read the documentation and then experiment. 
Software documentation is never exhaustive if the toolset is powerful - 
otherwise, it would grow exponentially unwieldy as the number of 
different user choices grows.

A few minutes' thought will suggest ways you can test to see if any 
fitting is occurring.


> On Tue, Feb 16, 2010 at 3:54 PM, Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at 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 at gromacs.org
>     <mailto:gmx-users at 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-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/mailing_lists/users.php

More information about the gromacs.org_gmx-users mailing list