# [gmx-users] Re: plotting the displacement of each C-alpha along first eigenvector having largest eigenvalue

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Aug 1 10:31:30 CEST 2008

```Hi,

A displacement is not a fluctuation. Displacement is also relational,
so you'll have to specify with respect to what. Likely you'd interpret
displacement with respect to the mean structure, which by definition
is at zero on a given principl axis. But in that case, the
displacement is more commonly referred to as the projection (option
-proj of g_anaeig) on that axis. The rmsf is the standard-deviation
(well, more correctly the square root of the second moment) of the
displacement/projection.

When using covariance analysis in MD, make sure first to understand
what it is; read some texts from statistics to get a good grasp.

Cheers,

Tsjerk

On Fri, Aug 1, 2008 at 10:05 AM, Bert de Groot <bgroot at gwdg.de> wrote:
> sunita gupta wrote:
>>
>> Hello
>>
>> I have a query that how to do PCA which further includes *plotting the
>> displacement of each C-alpha along first eigenvector having largest
>> eigenvalue*. I read in many articles that this can be done using gromacs. I
>> did my MD simutaion using charmm forcefield and NAMD. I have converted my
>> *dcd file trr* and using *g_covar *covariance analysis. But i am not getting
>> anything regarding displacement calculation....
>>
>> In GROMACS 3.1 manual their is an option of *-disp* is given with
>> *g_anaeig* command...but in 3.2 and 3.3. no such information is given and
>> its considering as invalid argument.
>>
>> Also someone mailed me that calculating the displacement along
>> eigenvectors is same as rmsf (root mean square fluctuation) and it can be
>> calculated using -rmsf option in g_anaeig commant......Kindly help me in
>> this regard and clear my doubts...
>>
>
> g_anaeig -rmsf
> seems a perfectly valid suggestion to me. What's your doubt?
>
>
> Bert
>
> ______________________________________
> Bert de Groot, PhD
>
> Max Planck Institute for Biophysical Chemistry
> Computational biomolecular dynamics group
> Am Fassberg 11
> 37077 Goettingen, Germany
>
> tel: +49-551-2012308, fax: +49-551-2012302
> http://www.mpibpc.mpg.de/groups/de_groot
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University