Hi Dr.Roe,
I tried the way you specified above. As I can understand,it dumps the three
vectors for velocities, three for coordinates and then another three for
velocity+coordinates. So I guess there is no default way to do an
autocorrealtion study based on distance between two atoms.
Thank you
Sajeewa Dewage
On Thu, May 16, 2013 at 5:53 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu May 16 2013 - 16:00:03 PDT
