Re: [AMBER] ncorr in rotdif command seems redundant to me. Please help.

From: Daniel Roe <>
Date: Tue, 3 Nov 2015 20:38:15 -0700

On Tue, Nov 3, 2015 at 6:49 PM, case <> 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.


> ....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
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Nov 03 2015 - 20:00:03 PST
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