On 10/11/2011 5:36 PM, James Starlight wrote:
Thank you, Mark.

By the way, also I have some question about data analysing

From g_anaeig  I can obtain atom fluctuations along defined mode



1- Can I obtain same fluctuations along ensemble of several modes (i.e averaged fluctuations along modes from n to k ) in one graph ?

Yes, through suitable use of your graphing program on multiple input files. IMO that would not be a suitable discussion for this list. Suggestions for graphing programs and some tricks of the trade are on the GROMACS webpage.


2- Is there any way to obtain fluctuations of C-alpha atoms or backbone only from full atomic model ?
E.g on start g_anaeig ask me

Select an index group of 6518 elements that corresponds to the eigenvectors
Group     0 (         System) has  6518 elements
Group     1 (        Protein) has  6518 elements
Group     2 (      Protein-H) has  3269 elements
Group     3 (        C-alpha) has   413 elements
Group     4 (       Backbone) has  1239 elements
...

but I can chose only full atomic representation of the system consisted of 6518 atoms and any other selection would produce error. Is there any other way to obtain fluctuations on reduced number of atoms from full-atomic system ?

Unless g_nmeig can be persuaded to calculate on a subset of the Hessian, I would guess not.



3- Also I've done two different NMA from one reference ( for full atomic model and for C-alpha mode). The overal picture of RMSF for instance was overal in both of the analysis but in case of the C-alpha only ANM RMSF were bigger in 10 times (0.02 Nm in case of full atomic NMA vs 2 NM in case of C-alpha NMA on equat residues).
Why that difference might occur?

From your description, I think you're comparing apples with oranges.

Is there any way to increase amplitude of fluctuations by the temperature rising for instance ?

 NMA is athermal.

Mark
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