AMBER Archive (2009)Subject: [AMBER] analysis on Amber
From: oguz gurbulak (gurbulakoguz_at_gmail.com)
Date: Sat Mar 07 2009  12:04:19 CST
Dear Amber Users,
I'm interested in evaluating thermophysical and rheological properties of
nalkanes and binary mixtures of nalkanes. I performed md simulations using
Amber 10 v. and I want to do analysis with my Amber trajectory files. My
aim is to get Self Diffusion coefficents from calculating MSD and velocity
autocorrelation functions and to get shear viscosity from calculating the
autocorrelation functions of the stress tensors. For this reason, I
searched Amber manuals, tutorials and mail archives in order to have enough
information about these operations. I learned that ''diffusion'' command in
ptraj can calculates MSD and 'analyze timecorr' option of ptraj can
calculates time correlation functions. I read this part of Amber manual, but
I didn't see any procedure in order to calculate velocity autocorrelation
functions. According to me part of the problem is likely because velocities
are not output into the mdcrd files. I thought that I can do this manually
by first outputting different restart files instead of overwriting them.
Then manually extracting velocities and calculating the autocorrelations. Am
I right ? Could you please give me the right information about this
operation ? How can I calculate velocity autocorrelation functions in ptraj
?
Ptraj input files :
trajin foo.mdcrd
trajout restart restart
trajin foo.mdvel
trajout restart restart
And, in order to get shear viscosity I need to obtain the autocorrelation
functions of the stress tensors. But I didn't find any information on this
procedure. Is it right that Amber can't calculate the autocorrelation
functions of the stress tensors ? If so, I thought that if I can to get the
calculated accelerations and pressure tensor elements at the end of each
record of md simulation, I can manually calculate shear viscosity by myself.
I think Amber must have written the calculated accelerations and pressure
tensor elements at the end of each record of md simulation. But the problem
is how can I extract these informations as a output file. Ưn this point I
strongly need your help to learn much about this procedure. Is there a way
to extract these informations as a output file ?
Thanks in advance.
Sincerely
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