Dear Jason,
I shall try to learn using pytraj in near future.
Thanks for your suggestion anyway.
Regards
Vijay
On Wed, Mar 25, 2015 at 9:52 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Wed, Mar 25, 2015 at 7:42 AM, Vijay Achari <glycoamber.gmail.com>
> wrote:
>
> > Dear Sir,
> >
> >
> > I am trying to calculate autocorrelation function.
> >
> > Normally I use a to run the calculation (shown below: SCRITP(I)). This
> > script run in loop. Each time it load the trajectory file using trajin
> and
> > does the calculation.
> >
> > Instead I would like to load the trajectory only once and do the
> > calculation loop-wise as shown in SCRIPT(II). When I tried to run the
> > SCRIPT(II), I get error message as below:
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > *CPPTRAJ: Trajectory Analysis. V14.25 ___ ___ ___ ___ | \/ |
> \/ |
> > \/ | _|_/\_|_/\_|_/\_|_ Reading
> > '../../../../only-nc-Format-bcmLyo25perR/bcmLyo25perR.prmtop' as Amber
> > TopologyINPUT: Reading Input from STDIN [trajin
> > ../../../../only-nc-Format-bcmLyo25perR/md-all-bcmLyo25perR.nc 15000
> > 60000] Reading
> > '../../../../only-nc-Format-bcmLyo25perR/md-all-bcmLyo25perR.nc' as Amber
> > NetCDF [unwrap *] UNWRAP: By atom using mask '*' Reference is
> first
> > frame. [for j in {1..128};do]'for': Command not found. 1 errors
> > encountered reading input.TIME: Total execution time: 0.0695 seconds.*
> >
> > Is that possible to run the for command from cpptraj command?
> >
>
> No. It is not (currently) supported. Also, I'm not sure how you are
> pasting the output into your email client, but it is coming out mangled,
> making it very hard to decipher and easy to miss important details.
>
>
>
> > Or is that any other way to do the calculation by reading the TRAJECTORY
> > only once and do the repeated calculation iteratively?
> >
>
> There are two options that I can think of. The first is to use your loops
> in shell scripting to write a cpptraj script, then run that serialized
> script directly. Another way, if you are familiar with Python, is to use
> pytraj (http://github.com/pytraj/pytraj), which will give you access to
> all
> of cpptraj's functionality combined with the Python interpreter and numpy
> library.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Wed Mar 25 2015 - 10:00:03 PDT
