[gmx-users] Re: from nur

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Nov 2 09:08:43 CET 2006

Hi Nur,

For each analysis program in gromacs you can get an explanation from
the manual and by issuing the command with the option -h. In many
cases you will find a pointer to an article in which the method (and
its interpretation) is explained.

The RMSD (root mean square deviation) is a measure of the distance
between two configurations of a system in conformational space. The
closer two conformations are, the smaller is the RMSD, indicating that
the structures have a high degree of similarity. Note that, for a
given reference structure, there are only a limited number of similar
structure, while the number of structures increases rapidly with
increasing RMSD. Therefore, two structures which have a low RMSD
against a given reference structure are also similar to each other,
but for two structures with a high RMSD the value is basically

Maybe it's a good point to add more explanation regarding the meaning
of the analysis in the tutorial. I will have a look at it at some

Anyway, it is also good to have clear that there is little point in
just doing loads of analysis on your system without having a certain
aim in mind. Trying to make sense of it afterwards and finding a
question to fit your answers is difficult and rather silly. First,
define your problem, and rephrase it as a question. Think of the data
you need to answer your question. Infer which analysis tools you could
use to extract the data needed from your simulations and from this
determine the requirements for, the set up of your simulation.

Hope it helps,


On 11/1/06, nur avneet <nuravneet at yahoo.co.in> wrote:
> dear tsjerkw
> thanx for ur guidance n suggestions.
> i followed the tutorial...and its analysis too....but it does not tell
> anything about how to interprate the results...for eg i calculate the rmsd
> but how to interprate what i get...what does it tell about my simulation.
> i hope i am not disturbin or bothering u. do let me know if so....
> I am totally new to gromacs and need some guidance to know if i am goin in
> the right direction.
> Please...if u could devote little time.....
> thanx
> Regards
> nur
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Tsjerk A. Wassenaar, Ph.D.
NMR, Utrecht University,
Padualaan 8,
3584 CH Utrecht, the Netherlands
P: +31-30-2539931
F: +31-30-2537623

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