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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Received on Thu May 16 2013 - 14:30:03 PDT
