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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