Ben,
Thank you very much for your advice. I appreciate it.
Regards,
Surasak
> From: ben.roberts.geek.nz
> Date: Sat, 21 Jan 2012 12:31:45 -0500
> To: amber.ambermd.org
> Subject: Re: [AMBER] Calculate the cosine content of PC
>
> Hi Surasak,
>
> On 16/01/2012, at 5:44 AM, surasak chunsrivirot wrote:
>
> >
> >
> >
> >
> >
> > Hi,
> >
> > I'm trying to compute the cosine content of the first PC from the
> > principal component analysis of a trajectory (10,000 frames). I'm
> > wondering if AMBER has a tool that helps with this calculation.
> >
> >
> >
> > I tried using this script to generate an eigen vector of the first PC.
> >
> >
> > trajin ../alav.bps
> >
> > matrix covar name covmat out covmat-ca.dat .CA
> >
> > analyze matrix covmat out evec1-ca.dat vecs 1
>
> One possibility - a bit kludgy, but probably better than nothing - would be to use a script to generate a series of ptraj files, each with a trajin command dealing with only one frame. Because you can use trajin to read in a subset of the trajectory. My suggestion would be to look up the syntax of the trajin command, then to use something like perl, python or a shell language (e.g., bash) to generate the necessary ptraj input files.
>
> HTH,
> Ben
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Received on Thu Jan 26 2012 - 20:00:02 PST
