[gmx-users] TRACE OF RMSD COMPARISON MATRIX

[Richa Singh]

Thankyou!! sir. Your answer helped a lot.

Richa

On 2 July 2013 13:04, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> Hi Richa,
>
> >From your explanation, I understand you want to know the sum of distances
> between each frame and its corresponding filtered frame. I think it makes
> more sense to sum squared distances, but that's a minor detail.
> The (non-mass-weighted) RMSD between two structures, written as positional
> vectors in 3N dimensional space, and properly rotated is:
>
> RMSD(a,b) = sqrt((a-b)'(a-b))
>
> In your case, the objective is comparing a frame x and the frame filtered
> by a set of eigenvectors, represented as the skinny matrix P: y = PP'x
>
> So, because the structures were fit prior to the covariance analysis
> anyway, the MSD is
>
> MSD = (x-PP'x)'(x-PP'x) = x'x + x'PP'PP'x - 2x'PP'x
>
> Because the eigenvectors are an orthonormal set, P'P = I and we get
>
> MSD = x'x - x'PP'x
>
> Now, x'x is just the radius of gyration squared of the original structure,
> so you can easily get that with g_gyrate for your trajectory. x'PP'x is the
> inner product of the projections of x onto the eigenvectors in P, which you
> get with g_anaeig -proj. So your objective is easily reached with some
> relatively cheap calls to g_gyrate/g_anaeig and a bit of scripting in awk
> or python, avoiding the determination of a whole RMSD matrix, just to get
> the trace. In fact, it becomes rather trivial to do this for any subset of
> eigenvectors you desire.
>
> As for the final answer, I would sum the MSD and take the square root,
> rather than summing the square roots, to get a more meaningful answer. But
> it's already unclear to me what these numbers would signify to begin with.
>
> Hope it helps,
>
> Tsjerk
>
>
>
>
> On Tue, Jul 2, 2013 at 8:53 AM, Gaurav Goel <gauravgoeluta at gmail.com> wrote:
>
>> Following link might be helpful:
>> http://orbeckst.github.io/GromacsWrapper/gromacs/core/fileformats/xpm.html
>>
>> -g
>> --
>> Gaurav Goel
>> Assistant Professor
>> Department of Chemical Engineering
>> Indian Institute of Technology, Delhi
>> Hauz Khas, New Delhi 110016
>> India
>>
>> On 02-Jul-2013, at 10:45 AM, Richa Singh <richa.s.rathorerr at gmail.com>
>> wrote:
>>
>> > Hello users,
>> >
>> > I'm using g_rms to compare my actual trajectory obtained from
>> > simulation with the filtered trajectory (along given set of
>> > eigenvectors), this gives me an RMSD comparison matrix in xpm format
>> > where the values of the plot are not clear. Is there any way which can
>> > help me to get the values along the diagonal of the matrix?
>> > the command that i followed is:
>> > g_rms -s ref.tpr -f actual.xtc -f2 filtered.xtc -m rmsd.xpm
>> >
>> > I want to calculate the trace of the matrix basically.
>> >
>> >
>> > Regards..
>> > --
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
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