Hi,
On Thursday, May 16, 2013, Sajeewa Pemasinghe wrote:
> 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.
Calculating the autocorrelation function for a scalar data set like distance
is different than for a vector. If you just want autocorrelation for a
distance use the 'corr' command.
-Dan
>
> Thank you
>
> Sajeewa Dewage
>
>
>
> On Thu, May 16, 2013 at 5:53 PM, Daniel Roe <daniel.r.roe.gmail.com<javascript:;>>
> 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<javascript:;>
> >
> > 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 <javascript:;>
> > > 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)
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org <javascript:;>
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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> AMBER.ambermd.org <javascript:;>
> 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 - 16:00:03 PDT
