From: Jose Borreguero <borreguero.gmail.com>
Date: Wed, 4 Nov 2015 06:28:43 -0500

Dear dac & dan,

Thanks for your clarifications, now I understand the role of ncorr. I'll be
reading also Wong & Case's paper.

I was also wondering if there was any kind of "ensemble average" when
calculating the correlation function by averaging over different trajectory
chunks. For instance, if ncorr=1000 then calculating C(t) over frames
[0,1000], [1000,2000], [2000,3000],... and then doing the average of these
C(t)'s. From what I gather this average is not an option right now, correct?

-Jose

On Tue, Nov 3, 2015 at 10:38 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:

> On Tue, Nov 3, 2015 at 6:49 PM, case <david.case.rutgers.edu> wrote:
> > On Tue, Nov 03, 2015, Jose Borreguero wrote:
> >>
> >> I am using the difrot command for the first time. I have read the manual
> >> and I can't understand the purpose of "ncorr" that is not accomplished
> with
> >> ti and tf.
>
> For historical reasons (i.e. because it was implemented this way in
> the original fortran code from Vance Wong that I adapted for cpptraj),
> ncorr is the max number of frames to calculate the time correlation
> functions for, and ti and tf delineate the portion of the time over
> which integration of the time correlation functions occurs. So if you
> have 10,000 frames and you set ncorr to 1000, the time correlation
> functions will only be calculated up to 1000 frames. If you specify
> your dt as 1 ps, you could then integrate from t0=0 ps to tf=1000 ps.
>
> > Dan: (a) calling ti the "initial time for calculating integral" is pretty
> > vague. (b) I think(?) that the description of ncorr in the documentation
> > is wrong: tf just needs to be less than (not "much less" that) ncorr*dt.
> > I'll take a stab at updating the documentation. (c) have ncorr input as a
> > frame number, but ti and tf as ns seems confusing.
>
> Ultimately the units of 'ti' and 'tf' and tstep just need to be
> consistent, i.e. if ti and tf are in ps then dt should be as well. The
> docs should definitely be changed to reflect this.
>
> -Dan
>
> >
> > ....dac
> >
> >
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>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
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Received on Wed Nov 04 2015 - 04:00:03 PST
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