[gmx-users] Block average RMSD using g_analyze

[Tsjerk Wassenaar]

Hi Anirban,

If you calculate the RMSD over a trajectory using g_rms and do block
averaging on the result, it won't give you any information about
convergence. The conformational space away from the reference structure
(>0.1nm, >0.5nm?) is just too big. This means that the protein can be
moving a lot, without showing in the RMSD.

Cheers,

Tsjerk


On Mon, Apr 22, 2013 at 12:00 PM, Anirban <reach.anirban.ghosh at gmail.com>wrote:

> Hi ALL,
>
> In order to see the convergence of a trajectory I am trying to calculate
> the RMSD error estimate using block averaging method which is implemented
> using g_analyze with -ee option. In it can I manually provide the block
> size or is it calculated based on the total simulation time? Another thing,
> is this method same as the block average RMSD method outlined by Alan
> Grossfield in JCTC 2011:7;2464-2472, in order to test convergence of a
> trajectory?
> Any suggestion is welcome.
>
> Regards,
>
> Anirban
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-- 
Tsjerk A. Wassenaar, Ph.D.