[gmx-users] Re: RE : essential dynamics

[bharat gupta]

I searched the user list in order to get some idea about calculating cosine
content of first PCA .. but I am not able to do so ??

Can u direct me to a good thread or discussion..


On Tue, Feb 1, 2011 at 2:04 AM, bharat gupta <bharat.85.monu at gmail.com>wrote:

> Thanks for the reply ...
>
> I am following this thread -
> http://oldwww.gromacs.org/pipermail/gmx-users/2004-May/010438.html
>  <http://oldwww.gromacs.org/pipermail/gmx-users/2004-May/010438.html>Also
> I read the following paper http://pubs.acs.org/doi/abs/10.1021/jp983120q (Internal
> dynamics of GFP) in which they have carried out such projections of the
> eigen vector in order to find the regions showing minimum and maximum
> amplitudes..
>
> What I am thinking is shall I take those c-alpha atoms that are well stable
> and equilibrated after referring to RMSD graph generated after simulation
> ...
>
> I am stating here what I have done so far and what I have to analyze :-
>
> I exchanged the loops regions of GFP with loops of longer length taken from
> pdb .. I simulated both the crystal str. and modeled strs. to compare how
> the loop incorporation leads to the change in the structure of GFP ....
> Since the RMSD of the GFP crystal str and that of model are in comparable
> range .. I thought of looking at the motions of loops in the structure that
> are giving such fluctuations in RMSD of model and for that I decided to
> generate eigen vectors and project them in 3d (like the one given in paper
> mentioned above) to see how that particular loop behaves .. I don't know
> whether what I have hypothesized is correct or not .. since I am not able to
> find any other insilico method apart from MDS for such a study .. Also if my
> prediction comes out to be good enough I have to carry out such insertion in
> the wet lab and has to check for fluorescence ..any help in this regard will
> be appreciated...
>
>
> On Tue, Feb 1, 2011 at 1:28 AM, Tsjerk Wassenaar <tsjerkw at gmail.com>wrote:
>
>> Hi Bharat,
>>
>> On Tue, Feb 1, 2011 at 8:33 AM, bharat gupta <bharat.85.monu at gmail.com>
>> wrote:
>> > Hi,
>> > After searching though gmxuserlist I found the relevant thread for ED...
>> I
>> > followed the following steps :-
>>
>> What thread are you referring to?
>>
>> > 1) g_covar - to generate a covariance matrix and diagonalize it (for
>> c-alpha
>> > atoms only)
>> > 2) g_anaeig - to generate eigen vectors
>>
>> g_covar calculates the eigenvectors. It's what you end up with through
>> diagonalization.
>>
>> > 3)g_rmsf - for calculating RMSD of first 8 eigen vectors , I got an
>> error at
>> > this step that -
>>
>> g_rmsf is not for calculating RMSD, and hasn't got much to do with
>> eigenvector analysis. That's what g_anaeig is for (like with the
>> option -rmsf). Using g_anaeig will avoid the error you observe.
>>
>> As a side note, 3 ns is rather short for this sort of thing. You have
>> to check the cosine content of the first principal components to see
>> if you've reached equilibrium already.
>>
>> Cheers,
>>
>> Tsjerk
>>
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>> post-doctoral researcher
>> Molecular Dynamics Group
>> * Groningen Institute for Biomolecular Research and Biotechnology
>> * Zernike Institute for Advanced Materials
>> University of Groningen
>> The Netherlands
>> --
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>
>
>
> --
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343
> Mobile no. - 010-5818-3680
> E-mail : monu46010 at yahoo.com
>
>


-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46010 at yahoo.com
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