[gmx-users] Cross-correlation map of protein residues

[Ebert Maximilian]

Thanks for your reply. I saw it and tried to change the code to work with gromacs 5 but my output plot doesn’t seem right. the code is written for gromacs 3.3 and is not easily build agains 5. do you have a version working on 5?

thanks

> On Jul 18, 2015, at 1:32 AM, bipin singh <bipinelmat at gmail.com> wrote:
> 
> There is a modified version of g_covar available at the below link for
> calculating correlation matrix:
> 
> http://www.gromacs.org/Downloads/User_contributions/Other_software
> 
> http://www.gromacs.org/@api/deki/files/55/=g_covar.tgz
> 
> 
> ------------------------------
> Thanks and Regards,
> Bipin Singh
> 
> On Fri, Jul 17, 2015 at 6:51 PM, Ebert Maximilian <m.ebert at umontreal.ca>
> wrote:
> 
>> Dear list,
>> 
>> I am looking for a gromacs tool which is able to calculate/draw a map of
>> residues which are either in their motion correlated or anti correlated.
>> first i thought i could just use g_covar with c-alpha and use the -xpma
>> option but while reading previous mailing list posts people said that the
>> atomic covariance matrix does not correlate motions. All posts I found
>> where older and the script from the gromacs site for a g_covar tool which
>> can calculate the correlation plot is from 2009. Therefore, i wanted to
>> know if gromacs 5 is able to directly calculate the plot. if not does
>> anybody know a straight forward way of doing so for a gromacs trajectory?
>> 
>> thank you very much,
>> 
>> max
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