[gmx-users] Cross-correlation map of protein residues
m.ebert at umontreal.ca
Wed Jul 22 16:11:55 CEST 2015
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?
> 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:
> Thanks and Regards,
> Bipin Singh
> On Fri, Jul 17, 2015 at 6:51 PM, Ebert Maximilian <m.ebert at umontreal.ca>
>> 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,
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