[gmx-users] domain

[Anton Feenstra]

smith wrote:

>   
> Dear gmx users and David sir, 
>     
> I have performed a 10 ns md on a enzyme with two domain structure  
> using gromacs.After the simulation, visualising one of the structures  
> picked with largest rmsd showed variation (some movement) of one  
> domain with respect to other.I want to quantitatively measure the  
> rotation angle of one domain with respect to other, basiclly analyse  
> it.  
>   
> *Is there any tool avilable in gromacs to analyse this conformational  
> change.  
> *Can dyndom be used for this purpose by giving the minimized  
> structure and md structure as pdb1(conformer1) and pdb2(conformer2)  
> and result obtained.  
>   
> *I have not performed Essential dynamics on gmx trajectories, is it  
> necessary.  
>   
> Can results given by dyndom be interpreted and acceptable for MD  
> simulation.  

Yes, you can use DynDom for analysis of MD simulations. Most useful way
is to first do ED analysis, and then DynDom on (several) eigenvector(s),
by first projecting the extremes as a pair of .pdb file (use g_anaeig),
and feeding the pair of .pdf files to DynDom.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
|             | "If You See Me Getting High, Knock Me Down" (RHCP)    |
|_____________|_______________________________________________________|