In cpptraj, an example is:
vector v1 :1.CA :100.CA
timecorr vec1 v1 out v1.dat
See the AmberTools 13 manual for a more detailed explanation and more options.
-Dan
On Thu, May 16, 2013 at 3:19 PM, Sajeewa Pemasinghe <sajeewasp.gmail.com> wrote:
> Hi everyone,
>
> I want to calculate the distance between two particular atoms (For example
> :1 .A and :100 .B) with respect to time throughout the MD simulation.
> And then using this time-series data I want to calculate the
> autocorrelation function in order to calculate the correlation time (or the
> relaxation time).
>
> In the AmberTools manual, the calculation of time-correlation function is
> described as
>
> analyze timecorr vec1 vecname1 vec2 vecname2 .......(other
> options)
>
> So I have to generate a vector which keeps track of the distance between
> the two atoms (:1.A and:100.B).
>
> The specification of vector is given in AmberTools as
>
> vector name mask1 mask2 ....(other options)
>
> When I followed the description I couldn't understand how to specify a
> vector that would keep track of the distance between two atoms.
>
> Could anyone help me out in figuring out how to generate a vector file
> that would contain the distance information between two atoms during the
> simulation?
>
> Thank you
>
> Sajeewa Dewage
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> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Thu May 16 2013 - 15:00:03 PDT
