<div dir="ltr">Dear Xavier,<br><br>Thank you very much for your valuable inputs. I am extremely sorry for troubling you quite often.<br><br>You are absolutely right and I am using the second order legendre polynomials to obtain the correlation function only (am not using this to fit the correlation function data). The correlation function vs time curve I obtained is an exponentially decaying function. I am integrating this data (variation of correlation functions with time) for obtaining the correlation time. Probably I am making mistake here but am not sure. <br>
<br>""For an NH vector of the backbone there are several motion model that one has to decide<br>
which one is best""<br><br>You mean to say that, I need to use any of the model to fit the correlation function vs time data to obtain the relaxation time for N-H curve. <br><br>Thanks and Regards,<br>Ram.<br><br>
<div class="gmail_quote">On Fri, Sep 5, 2008 at 4:08 AM, Xavier Periole <span dir="ltr"><<a href="mailto:X.Periole@rug.nl">X.Periole@rug.nl</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
On Thu, 4 Sep 2008 21:13:39 -0400<div class="Ih2E3d"><br>
"rams rams" <<a href="mailto:rams.crux@gmail.com" target="_blank">rams.crux@gmail.com</a>> wrote:<br>
</div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Xavier,<br>
<br><div class="Ih2E3d">
I have a question about the accuracy of the correlation times obtained using<br>
gromacs tools. (I am getting these by integrating the output .xvg file of<br>
g_rotacf using g_analyze). Since the experimental values are not available<br>
to compare, I am not so sure about the correlation times I am getting. They<br>
are of the order of 0.4 to 0.8ns for various N-H vectors. I believe the<br>
values depends upon the range of time frames we use to fit with the legendre<br>
polynomials. I am using second order legendre polynomial to fit the frames.<br>
Can you give me any general suggestions to follow to obtain the reasonable<br>
correlation time values with MD simulations.<br>
</div></blockquote>
The range of values depend on the molecule you look at and the solvent<br>
viscosity. A protein with 50-100 AA would have an experimental rotational<br>
correlation time around 3-5 ns. In MD you find in general faster motion (1-3<br>
ns may be) which is due to the solvent and may be solvent-protein interactions<br>
that are a bit too weak, but this is not completely understood.</blockquote><div> I am more concerned about the procedure you actually use to obtain your value.<br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
The Legendre polynomial should be of the order 2 if you compare to NMR<br>
relaxation data, this is ok, but you do not use to fit the data! You use it<br>
to build the correlation function. Then you fit the correlation function<br>
with a function that would describe the motion you look at! For an NH vector<br>
of the backbone there are several motion model that one has to decide<br>
which one is best. Have a look at that paper. I did not read it but it<br>
talks about model to fit NMR data and should contain a lot of reference<br>
for you to begin with. DOI: 10.1021/jp8038576.<br>
<br>
Then you should have look at your correlation functions. Are they converged<br>
(reached a plateau)? How do they look?<br>
<br>
You can also use the g_dipole to get the auto correlation function of the<br>
molecule dipole ...<div><div></div><div class="Wj3C7c"><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Ram.<br>
<br>
On Thu, Sep 4, 2008 at 11:02 AM, Xavier Periole <<a href="mailto:X.Periole@rug.nl" target="_blank">X.Periole@rug.nl</a>> wrote:<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
On Thu, 4 Sep 2008 09:45:34 -0400<br>
"rams rams" <<a href="mailto:rams.crux@gmail.com" target="_blank">rams.crux@gmail.com</a>> wrote:<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Xavier,<br>
<br>
I am extremely sorry for incomplete information. But this is a follow up<br>
to<br>
my previous two emails. Unfortunately I havent received any suggestions<br>
for<br>
them and it appears like you too missed them. For more clarity I am<br>
pasting<br>
them here again:<br>
<br>
</blockquote>
Well if you do not get an answer that is probably that your post is not<br>
really asking a quick "answerable" question and you might want to<br>
re-formulate your post or dig a bit to make things easier.<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
To calculate the rotational auto correlation functions, the command<br>
mentioned in the maual is:<br>
<br>
g_rotacf -P 1 -nparm 2 -fft -n index -o .xvg -fa -beginfit -endfit<br>
<br>
what are the -nparm and -fa options are meant for ?<br>
<br>
</blockquote>
This is an old exemple ... a bad one! Those options do not seem to exist<br>
anymore! Never knew they existed!<br>
you can grep "\-nparm" and "\-fa" in tools/*.c and you'll see they<br>
only appear in gmx_rotacf.c<br>
anyways These things are probably taken care of more invisibly.<br>
-nparm seems to give the number of parameters in the function to fit<br>
-fa the function to fit<br>
<br>
now: -nparm do not exist and -fa is -fitfn, most likely!<br>
<br>
This exemple should be removed and replaced! Just look at the<br>
options\listed when you type g_rotacf -h.<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Also do we need to use -fitfn option to obtain the rotational auto<br>
correlation functions ??<br>
<br>
</blockquote>
No, -fitfn defines the type of function you'd use to fit the correlation<br>
function, which itself is written cause -o rotacf.xvg ...<br>
<br>
XAvier.<br>
<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Ram.<br>
<br>
<br>
<br>
<br>
<br>
Dear users,<br>
<br>
I have given a command like the following to calculate the rotational auto<br>
correlation function:<br>
<br>
g_rotacf -f .trr -s .tpr -P 2 -fft -o .xvg -b 0000 -e 10000 -n .ndx -d<br>
<br>
I want to use the second order Legendre polynomial to fit. I integrated<br>
the<br>
resulting .xvg file, to obtain the correlation time using:<br>
<br>
g_analyze -f .xvg -integrate<br>
<br>
The output is the following. Could some one help me in understanding it<br>
betterly.<br>
<br>
Calculating the integral using the trapezium rule<br>
Integral 1 120.92840 +/- 0.00000<br>
std. dev. relative deviation of<br>
standard --------- cumulants from those of<br>
set average deviation sqrt(n-1) a Gaussian distribition<br>
cum. 3 cum. 4<br>
SS1 2.428352e-02 2.972849e-02 4.204243e-04 9.301 120.228<br>
<br>
<br>
Which value corresponds to correlation time and in which units (its in ps<br>
I<br>
suppose) ?<br>
<br>
Thanks in advance.<br>
<br>
Ram.<br>
<br>
<br>
On Thu, Sep 4, 2008 at 2:32 AM, Xavier Periole <<a href="mailto:X.Periole@rug.nl" target="_blank">X.Periole@rug.nl</a>> wrote:<br>
<br>
On Wed, 3 Sep 2008 23:40:14 -0400<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
"rams rams" <<a href="mailto:rams.crux@gmail.com" target="_blank">rams.crux@gmail.com</a>> wrote:<br>
<br>
Hi,<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
I am so surprised for not finding any one who have better experience<br>
with<br>
g_rotacf. I have been playing around with it and the time correlation<br>
value<br>
I got by g_rotacf is so small in comparison to the time correlation<br>
value<br>
I<br>
calcualted using the hydrodynamic radius of the protein. The value is<br>
nearly<br>
10 times less. Can some one give me a better idea about g_rotacf.<br>
<br>
Many people have certainly used g_rotacf to get ACFs of different<br>
</blockquote>
observables.<br>
<br>
Anyways the way you describe your system, command line and your problem<br>
does<br>
does not help anyone to help you. Read your message above and think about<br>
what<br>
you would answer! You've played around with g_rotacf therefore you know<br>
it<br>
is not straightforward to give you the magic command.<br>
<br>
XAvier.<br>
<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Ram.<br>
<br>
<br>
</blockquote>
-----------------------------------------------------<br>
XAvier Periole - PhD<br>
<br>
Molecular Dynamics Group / NMR and Computation<br>
University of Groningen<br>
The Netherlands<br>
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-----------------------------------------------------<br>
XAvier Periole - PhD<br>
<br>
Molecular Dynamics Group / NMR and Computation<br>
University of Groningen<br>
The Netherlands<br>
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-----------------------------------------------------<br>
XAvier Periole - PhD<br>
<br>
Molecular Dynamics Group / NMR and Computation<br>
University of Groningen<br>
The Netherlands<br>
-----------------------------------------------------<br>
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