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