# [gmx-users] RMSIP

Tsjerk Wassenaar tsjerkw at gmail.com
Wed May 19 10:10:29 CEST 2010

```Hi,

The answer is given by g_anaeig (-h):

When -v, -eig, -v2 and -eig2 are given, a single number for the overlap
between the covariance matrices is generated. The formulas are:
difference = sqrt(tr((sqrt(M1) - sqrt(M2))^2))
normalized overlap = 1 - difference/sqrt(tr(M1) + tr(M2))
shape overlap = 1 - sqrt(tr((sqrt(M1/tr(M1)) - sqrt(M2/tr(M2)))^2))
where M1 and M2 are the two covariance matrices and tr is the trace of a
matrix. The numbers are proportional to the overlap of the square root of the
fluctuations. The normalized overlap is the most useful number, it is 1 for
identical matrices and 0 when the sampled subspaces are orthogonal.

A more elaborate explanation is given in chapter 8.10 of the manual.
The definition for the RMSIP is a different one, but can readily be
found in literature.

Cheers,

Tsjerk

On Wed, May 19, 2010 at 9:02 AM, Mark Abraham <mark.abraham at anu.edu.au> wrote:
>
>
> ----- Original Message -----
> From: pawan raghav <pwnrghv at gmail.com>
> Date: Wednesday, May 19, 2010 16:28
> Subject: [gmx-users] RMSIP
> To: gmx-users at gromacs.org
>
>> Thanks mark, but I think that g_anaeig calculates the degree of overlap then what method would you use to calculate this?>
>
> I don't know what you are asking, and I certainly don't know the answer :-).
>
> Mark
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--
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands

```