[gmx-users] Normal Mode Analysis
Mark.Abraham at anu.edu.au
Thu Nov 10 07:51:59 CET 2011
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
> 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.
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