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