[gmx-users] Normal Mode Analysis
jmsstarlight at gmail.com
Thu Nov 10 07:36:51 CET 2011
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 ?
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 ?
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
Why that difference might occur? Is there any way to increase amplitude of
fluctuations by the temperature rising for instance ?
2011/11/10 Mark Abraham <Mark.Abraham at anu.edu.au>
> On 10/11/2011 6:48 AM, James Starlight wrote:
>> I've another question about NMA.
>> 1- As I understood the Sparce matrix method is used on default in case
>> when my reference structure consist of alot of atoms. If this true the
>> output Hessian.mtx would be in sparce format, wouldn't it ?
>> 2- How I can convert output.mtx to the txt format ? As the consequence I
>> want to obtain something like this
> GROMACS is not very helpful with matrices of data, unfortunately. You can
> dump the numbers out of the .mtx format with gmxdump, but you would be on
> your own to then convert it to some other format you want (i.e. write some
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