[gmx-users] Normal Mode Analysis

James Starlight jmsstarlight at gmail.com
Thu Nov 10 08:04:10 CET 2011

Mark hello,

2011/11/10 Mark Abraham <Mark.Abraham at anu.edu.au>

> From your description, I think you're comparing apples with oranges.
I just want compare results of coarse grained NMA based on C-alpha only
with full atomic NMA.
I've already done that work and obtain that

1- overal picture of fluctuations is the same for both methods
2- in case of full atomic NMA overal motion is damped in comparison to the
C-alpha only NMA ( rmsf of fluctuations are greater in 10 times)

3 Finally I just want to obtain fluctuations on Calpha atoms only for my
full atomic NMA for better comparison with cg NMA (e.g representation on
one graph RMSF on Calpha atoms only for both methods  )


>  Is there any way to increase amplitude of fluctuations by the temperature
>> rising for instance ?
>  NMA is athermal.
> Mark
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