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

[Mark Abraham]

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