# Re: [AMBER] Covariance Matrix of residues center of mass

From: Guadalupe Alvarez <gualvarez.unsam.edu.ar>
Date: Thu, 18 Jul 2019 13:51:39 -0300

Thank you very much for the response. It was really helpful.

El miÃ©., 17 jul. 2019 a las 13:31, David A Case (<david.case.rutgers.edu>)
escribiÃ³:

> On Wed, Jul 17, 2019, Guadalupe Alvarez wrote:
>
> >I'm trying to compute the Covariance Matrix of residues center of mass,
> but
> >the cpptraj function "matrix covar" only performs the calculation by atom,
> >not by residue. Does anybody know a way for doing this?
>
> You can use the "vector" command to get the centers of mass of various
> groups, then use the "matrix covar" command on those. Here's an
> example:
>
> first step:
>
> parm ....
> trajin ....
> vector res1 center :1
> vector res2 center :2
> ....
> run
> writedata resvectors.nc vectraj trajfmt netcdf parmout resvectors.parm7
> noorigin res*
> go
>
> This creates a "trajectory" with just the centers of mass of each
> residue, along with the corresponding prmtop file.
>
> Then you can read this in and analyze in a second cpptraj run:
>
> parm resvectors.parm7
> trajin resvectors.nc
> matrix covar @1-60 out corrmat.dat name rescovarmat
> precision corrmat.dat 10 5 # experiment to see how much precision you
> need
> diagmatrix rescovarmat out resvecs.dat name corrdiag vecs 50 # if you want
> ....
> go
>
> Change "60" above to however many vector commands you had in the first
> run.
>
> It may be possible to combine both steps into a single cpptraj run, but
> I've never done that. And Dan or others may know of a more elegant way
> to do this.
>
> ...hope this helps....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jul 18 2019 - 10:00:02 PDT
Custom Search