[gmx-users] Normal Mode Analysis

James Starlight 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
>> http://www.csb.pitt.edu/prody/**_downloads/oanm_hes.txt<http://www.csb.pitt.edu/prody/_downloads/oanm_hes.txt>
> 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
> script).
> Mark
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111110/a3437545/attachment.html>

More information about the gromacs.org_gmx-users mailing list