[MMTK] mmtk Digest, Vol 64, Issue 3

Konrad Hinsen hinsen at cnrs-orleans.fr
Wed Sep 17 12:39:27 UTC 2008


On 16.09.2008, at 17:30, Saravana Prakash wrote:

> I have charmm based trajectories , i want to analyze the mode -  
> projected dynamics of few  of modes,  could you please tell me does  
> MMTK open source will do this calculation  and  could you please  
> let me know little descript on doing this  stuff.

Yes, MMTK can do this. Here is a recent paper describing such a study  
using MMTK:

	http://dirac.cnrs-orleans.fr/plone/publications/all-publications/ 
HK_2007

Basically, the steps are the following:

- Convert your CHARMM trajectory to MMTK's netCDF format. A suitable  
converter is available as part of the nMOLDYN package (http:// 
dirac.cnrs-orleans.fr/plone/software/nmoldyn/).

- Calculate the normal modes of your system. MMTK has lots of models  
and options for this. I suggest to start by looking at the examples  
provided with MMTK and on the Web site (http://dirac.cnrs-orleans.fr/ 
MMTK/using-mmtk/mmtk-example-scripts/)

- Calculate the projection of the trajectory onto some or all of the  
normal modes. You will have to write a Python script for this. I can  
provide an example, but it is likely that you will have to modify it,  
so you definitely will need to understand how it works.

- Analyze the mode-projected dynamics. This depends of course on what  
you are looking at, but in any case you will have to write Python  
scripts for that. You might want to use code from nMOLDYN for  
inspiration.

Konrad.
--
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Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: hinsen at cnrs-orleans.fr
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