[gmx-users] Request on help in ED method

[K.A. Feenstra]

Phew. Quite a bit of work to read through all that.
Find my answers after each of your questions, below.

Dmitry Egorov wrote:
[...]
>   First.
>   When I use option -ref in g_covar input I give in covar.log "wrote average
> structure to eigenvec.trr with t=0" although in manual one of two functions
> of -ref option is writing ref structure with t=0 to eigenvec.trr instead of
> average when -ref option is used.
>   Why in eigenvec.trr last frame has t=499, but not the 500 as in initial
> trajectory.xtc file ( data obtained after trjconv program with -sep
> option ) - plus original structure with t=-1 and average with t=0 - all is
> 501, but I think should be 502
> ( t=-1, t=0, and t= from 1 to 500 - where is structure No 500 ) ?

Isn't there a frame with t=-2 also?

>   Since in chapter 8 said that covariance analysis depends on what structure
> was used in analysis - how can I decide what is better - use average ore
> reference structure for covariance analysis ? Are here some recipes.

The default is the average structure. It depends on how large the
conformational differences are between your structures. If the
differences are relatievely small (e.g. protein still has same
overall fold), I'd expect it doesn't matter too much.

>   Second. Most problems I have with understandig g_anaeig program.
>   In manual said "When a trajectory is projected on eigenvectors, all
> structures are fitted to the structure in the eigenvector file if present,
> othrwise to the structure in the structure file". When I use in g_covar same
> structures for fitting and analysis I always have initial structure in
> eigenvec.trr file with t=-1 ( as described in g_covar manual chapter ). But
> when I attempt to use as follows "g_anaeig -v eigenvec.trr -f
> trajectory.xts -extr str.ext.pdb" without -s option ( there is reference
> structure in eigenvec.trr with t=-1 ) I give fatal error : no topol file.
> What is need in this file here ?

Atom and residue names are needed to write a .pdb file. These are not
in the .xtc file, and must be read from the structure file (option -s,
can be e.g. .pdb or .gro file).

>  Then could you give me more detailed description of -extr option. It is not
> clear how does extreme values calculation perform ( at the ideas level )-
> and what are these values. What is function of -max option - what other
> extreme values can be obtained with this option when its value is not equal
> to zero?

-extr gives you the structure from the trajectory at the time (or the
frame number, you don't have time in Concoord) where the projection
on your essential mode is maximal or minimal (as you could also see in
the -proj plots).

>  What functions of -2d and -3d options and in what they differ from -proj
> option and for what goals I can use this option ( except, probably, -proj -
> I think I understand main function of -proj option - it is needed for next
> cosine content calculation with g_analyse to asess are motions described by
> obtained eigenvectors not random - am I right in this question ? ) ?

In a 2d (or 3d) eigenvector plot you can see the correlation between
2 (or 3) eigenvectors. If you would e.g. analyse a circular motion of
a single particle, you get 2 eigenvectors which are fully correlated.
A simple 1d plot of each would give a cosine like plot, but a 2d plot
would reveal the correlation from the circular motion.

>  When I use -filt option I give the same amount of frames as in other
>  after g_covar ) trajectory files - ( last number is 499 ). Intuitively I
> supposed that after filtration number of frames should be decresed - how
> does filtration perform and what results I can obtain with this option?

With -filt you keep the same number of frames, except that motions of
the atoms are only 'allowed' inside the selected eigenvectors.

>   Other options as I believe I understand now, except, may be, -inpr
> options - how and in what situations its results may I use.

To compare results from e.g. two different simulations.

>   Third. Most main question - may I and if yes, how may I obtain end
> conformations of my original structure projected on eigenvectors and is it
> possible to obtain these conformations with the all ( not only C-alpha atoms
> that was used in g_covar for analysis ) atoms.

In principle, no, since there is no information for the motion of the
atoms that were not analysed in g_covar. But, if is possible to 'morph'
your original structure to fit all new Ca atom positions, creating
positions of all intermediate (other backbone, and the sidechain) atoms.
There is a program to do that, but I don't recall what it's name was.


-- 
Groetjes,

Anton
  ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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