[gmx-users] Re: Cross-correlation maps

[James Starlight]

Mark,

Is there any way to calculate such cross-correlations without
calculation of the covariance matrix ( from the MD trajectory
indirectly) ?
I've noticed that after processind of my trajectory with PCA method
some dynamics ( e.g fluctuations of the side-chains) are lost even
when I've analysed filtered.xtc from the first 50 principal
components. How I should analyse possible cross-correlations of the
fluctuations of the side-chains?

James

2012/8/27 Mark Abraham <Mark.Abraham at anu.edu.au>:
> On 24/08/2012 4:51 PM, James Starlight wrote:
>>
>> up :)
>> It's appeared two additional questions.
>>
>> 1) In addition to the pca's cross-correlation maps I wounder to know
>> about possibility of calculation of such cross-correlation's from the
>> trajectories indirectly without calculation of the covariance
>> matrices.
>>
>> 2) is there any way to calculate degree of fluctuations of side-chains
>> ( degree of  torsion's dynamics) from the different trajectories and
>> to compare it ?
>> E.g I have one protein in two different (apo and holo) forms. I've
>> calculated two trajectories for both structures and observed different
>> degree of dynamics in case of each structure ( e.g fluctuations in
>> case of apo form were  more frequent than in case of liganded form).
>> IS there any way to direct mesure and comprison of such side-chain's
>> dynamics for two trajectories?
>
>
> Yes, but not with GROMACS tools. You can generate a .tpr for use with that
> old version of g_covar with an old version of grompp in a manner similar to
> the way you generate one now, but there are bunch of details different. You
> may not require a .tpr, of course. Look at the file types for g_covar_mod -s
> in the output for -h.
>
> Mark
>
>
>>
>>
>> James
>>
>> 2012/8/15, James Starlight <jmsstarlight at gmail.com>:
>>>
>>> Dear Gromacs users!
>>>
>>>
>>> I want to obtain Cross-correlation maps ( for indication of the
>>> cross-correlated fluctuations of the residues).
>>> The example of such maps can be found here
>>> http://pubs.acs.org/doi/abs/10.1021/ja076046a
>>>
>>>   I found that modificied version of the G_covar from users
>>> contributions can do such things. But because of the older version of
>>> that program (3.3.3) I've obtained the below error using it with 4.5.5
>>> gromacs
>>>
>>>
>>> Reading file md_GO.tpr, VERSION 4.5.5 (single precision)
>>>
>>> -------------------------------------------------------
>>> Program g_covar_mod, VERSION 3.3.3
>>> Source code file: tpxio.c, line: 1192
>>>
>>> Fatal error:
>>> reading tpx file (md_GO.tpr) version 73 with version 40 program
>>> -------------------------------------------------------
>>>
>>>
>>> Is there newest versions of the G_covar for such things or
>>> alternativelly any others ways to calculate such correlations maps ?
>>>
>>> Thanks for help
>>>
>>> James
>>>
>
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