Re: Correlation matrix of the Ca atoms

From: Joshua Adelman (jadelman_at_berkeley.edu)
Date: Sun Feb 01 2009 - 23:56:04 CST

Hi Chandan,

Documentation for g_covar and g_anaeig can be found here:
http://www.gromacs.org/documentation/reference/online/g_covar.html
http://www.gromacs.org/documentation/reference/online/g_anaeig.html

and there is a little tutorial here:
http://www.mpibpc.mpg.de/groups/de_groot/compbio/p4/index.html

You just have to follow the installation directions that come with
gromacs like you would any sort of compiled software.

As far as preparing a trr from a dcd file, you would use catdcd:
http://www.ks.uiuc.edu/Development/MDTools/catdcd/

where you would create an index file in vmd of just the CA atoms, or
you could extract them from the correlation matrix afterward.

If this seems too complicated to do what you want, I would just write
a tcl script in VMD since you can align molecules to a reference and
extract positions from trajectories. See the VMD tcl documentation and
tutorials for examples.

Good luck.
Josh

On Feb 1, 2009, at 9:47 PM, sripad chandan wrote:

> hii joshua,
> thanks for your reply.
> is there any material available regarding this.
> i have never used gromacs.
> thanks alot again.
> chandan
>
> On Mon, Feb 2, 2009 at 10:52 AM, Joshua Adelman
> <jadelman_at_berkeley.edu> wrote:
>> I find that the easiest way to do this is to download and compile
>> the tools
>> that come with gromacs (http://www.gromacs.org/) and use g_covar and
>> g_anaeig to analyze the principal components. You can also write
>> out the
>> covariance matrix, and I believe there is also a variation of
>> g_covar in the
>> user contributed software that calculates the correlation matrix
>> directly.
>> There is probably other software out there, but gromacs has a lot
>> of nice
>> tools all in one place.
>>
>> You will have to convert your dcd file to trr, which is pretty easy
>> using
>> catdcd.
>>
>> Josh
>>
>>
>> On Feb 1, 2009, at 8:46 PM, sripad chandan wrote:
>>
>>> Friends,
>>> I want to calculate the Correlation matrix of the Ca atoms
>>> (motion) in
>>> a 5 ns simulation done on NAMD, so that the relationship of the
>>> residual and domain motion can be found out.
>>> Is there any possibility of doing it by NAMD/VMD?
>>> It will be very helpful if some one can give a suggestion atleast.
>>> Thanks alot.
>>> Chandan
>>>
>>>
>>> --
>>> Sripad Chandan Patnaik
>>> Research Assistant
>>> National Institute of Technology, Rourkela
>>> +91-9861668977
>>>
>>
>> ------------------------------------------------------------------------------------------------------
>> Joshua L. Adelman
>> Biophysics Graduate Group Lab: 510.643.2159
>> 218 Wellman Hall Fax: 510.642.7428
>> University of California, Berkeley http://nature.berkeley.edu/~jadelman
>> Berkeley, CA 94720 USA jadelman_at_berkeley.edu
>> ------------------------------------------------------------------------------------------------------
>>
>>
>>
>>
>
>
>
> --
> Sripad Chandan Patnaik
> Research Assistant
> National Institute of Technology, Rourkela
> +91-9861668977

------------------------------------------------------------------------------------------------------
Joshua L. Adelman
Biophysics Graduate Group Lab: 510.643.2159
218 Wellman Hall Fax: 510.642.7428
University of California, Berkeley http://nature.berkeley.edu/~jadelman
Berkeley, CA 94720 USA jadelman_at_berkeley.edu
------------------------------------------------------------------------------------------------------

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