[gmx-users] CRY-ED question

[Anton Feenstra]

Bert de Groot wrote:

> Ruben Martinez Buey wrote:
> 
>>> Hi all,
>>
>>
>> I would like to compare my MD/ED simulations with a CRY-ED analysis of 
>> my protein, but I only have two crystal structures. Can I correctly 
>> deduce the essential dynamics from only two experimental conformations?
>>
> 
> Only partially. Obviously, from a PCA in this case you'll get only one 
> (meaningful) eigenvector:
> the difference vector between the two conformations.
> But this can still be used in e.g. a comparison to a simulation.

Also, you can project these two X-ray structures on the first two
essential modes from your ED analysis on the MD simulation. That would
tell you if, e.g., the start of your simulation is mode alike to one
X-ray structure, and it e.g. progresses more towards the other during
the MD.


-- 
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 chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|