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

[Carla Jamous]

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.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
> 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.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100216/8ed860d8/attachment.html>