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 Sat Jan 21 2012 - 10:00:02 PST
