[gmx-users] R.M.S.I.P. between two halves of same simulation

[Tsjerk Wassenaar]

Hi Raja,

Of course it's possible. The question is, what is the probability that
you observe it. It seems you want to compare simulations. In that
case, single measurements are unlikely to be sufficient. Maybe you
want to check our paper (Wassenaar and Mark, JCC 27 p. 316, 2006). In
that paper we describe a model and method for robust statistical
comparison of simulations, also using RMSIP data.

Cheers,

Tsjerk

On 7/28/06, raja <raja_28 at fastmail.us> wrote:
> Hi Tsjerk,
> I computed r.m.s.i.p. between eigvectors trajectory for two halves of
> the same simulation, I expected it should be higher value than its other
> eigenvectors. But in my case it is showing less than the others, For
> example, please look at the below r.m.s.i.p matrix
>                      Wild      Mutant1     Mutant2   Mutant3
>
> Wild              0.630693     0.650160    0.65414   0.632176
>
> Mutant1              -            -            -        -
>
> Mutant2              -            -            -        -
>
> Mutant3              -            -            -        -
>
> Other values of the matrix not computed yet, but please comment on this
> output, Is it possible? For Wild Vs Wild of 2ns simulation run, I
> generated eigenvector trr file using g_covar program for first 0 to 1ps
> and it was repeated for 1ps to 2ps. and finally I used both trajectories
> to compute r.m.s.i.p. value.
>
> With thanks!
> B.Nataraj
>
>
>
> --
>   raja
>   raja_28 at fastmail.us
>
> --
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-- 

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336