On Thu, 4 Sep 2008 09:45:34 -0400
"rams rams" <[EMAIL PROTECTED]> wrote:
Hi Xavier,
I am extremely sorry for incomplete information. But this is a follow up to
my previous two emails. Unfortunately I havent received any suggestions for
them and it appears like you too missed them. For more clarity I am pasting
them here again:
Well if you do not get an answer that is probably that your post is not
really asking a quick "answerable" question and you might want to
re-formulate your post or dig a bit to make things easier.
To calculate the rotational auto correlation functions, the command
mentioned in the maual is:
g_rotacf -P 1 -nparm 2 -fft -n index -o .xvg -fa -beginfit -endfit
what are the -nparm and -fa options are meant for ?
This is an old exemple ... a bad one! Those options do not seem to exist
anymore! Never knew they existed!
you can grep "\-nparm" and "\-fa" in tools/*.c and you'll see they
only appear in gmx_rotacf.c
anyways These things are probably taken care of more invisibly.
-nparm seems to give the number of parameters in the function to fit
-fa the function to fit
now: -nparm do not exist and -fa is -fitfn, most likely!
This exemple should be removed and replaced! Just look at the options\listed
when you type g_rotacf -h.
Also do we need to use -fitfn option to obtain the rotational auto
correlation functions ??
No, -fitfn defines the type of function you'd use to fit the correlation
function, which itself is written cause -o rotacf.xvg ...
XAvier.
Ram.
Dear users,
I have given a command like the following to calculate the rotational auto
correlation function:
g_rotacf -f .trr -s .tpr -P 2 -fft -o .xvg -b 0000 -e 10000 -n .ndx -d
I want to use the second order Legendre polynomial to fit. I integrated the
resulting .xvg file, to obtain the correlation time using:
g_analyze -f .xvg -integrate
The output is the following. Could some one help me in understanding it
betterly.
Calculating the integral using the trapezium rule
Integral 1 120.92840 +/- 0.00000
std. dev. relative deviation of
standard --------- cumulants from those of
set average deviation sqrt(n-1) a Gaussian distribition
cum. 3 cum. 4
SS1 2.428352e-02 2.972849e-02 4.204243e-04 9.301 120.228
Which value corresponds to correlation time and in which units (its in ps I
suppose) ?
Thanks in advance.
Ram.
On Thu, Sep 4, 2008 at 2:32 AM, Xavier Periole <[EMAIL PROTECTED]> wrote:
On Wed, 3 Sep 2008 23:40:14 -0400
"rams rams" <[EMAIL PROTECTED]> wrote:
Hi,
I am so surprised for not finding any one who have better experience with
g_rotacf. I have been playing around with it and the time correlation
value
I got by g_rotacf is so small in comparison to the time correlation value
I
calcualted using the hydrodynamic radius of the protein. The value is
nearly
10 times less. Can some one give me a better idea about g_rotacf.
Many people have certainly used g_rotacf to get ACFs of different
observables.
Anyways the way you describe your system, command line and your problem
does
does not help anyone to help you. Read your message above and think about
what
you would answer! You've played around with g_rotacf therefore you know it
is not straightforward to give you the magic command.
XAvier.
Ram.
-----------------------------------------------------
XAvier Periole - PhD
Molecular Dynamics Group / NMR and Computation
University of Groningen
The Netherlands
-----------------------------------------------------
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-----------------------------------------------------
XAvier Periole - PhD
Molecular Dynamics Group / NMR and Computation
University of Groningen
The Netherlands
-----------------------------------------------------
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