<div dir="ltr">Hi David Van der Spoel,<br><br>You are right I missed the "dt" factor in the integral. Thanks a lot.<br><br>Ram.<br><br><div class="gmail_quote">On Mon, Sep 1, 2008 at 2:52 PM, David van der Spoel <span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</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;"><div class="Ih2E3d">rams rams wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Vitaly Chaban,<br>
<br>
The calcualted value of velocity autocorrelation function is 5.8*10^ -8 (momentum auto correlation function is 0.99279 and the protein mass is 4121.209 gm/mol). The resulting velocity auto correlation function will be in A^2/ps^2. If I devide this by a factor of 3, I will get the diffusion constant as 1.9 * 10^ -8 A^2/ps^2 which is nothing but 1.9 * 10^ -4 m^2/s^2. But the time factor in mean square displacement should be in m^2 sec^-1. Did I missed any thing here ?<br>
</blockquote></div>
yes. integration adds time in the denominator.<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
Ram.<div><div></div><div class="Wj3C7c"><br>
<br>
On Mon, Sep 1, 2008 at 11:54 AM, rams rams <<a href="mailto:rams.crux@gmail.com" target="_blank">rams.crux@gmail.com</a> <mailto:<a href="mailto:rams.crux@gmail.com" target="_blank">rams.crux@gmail.com</a>>> wrote:<br>
<br>
Dear Vitaly Chaban,<br>
<br>
Thanks for your kind sugestions. I did followed the way you<br>
mentioned for calcualting the diffusion constants. I like to have a<br>
better understanding of what I have done.<br>
<br>
g_velacc:<br>
<br>
g_velacc -f -s -o -aceflen<br>
<br>
Since, mine is a single protein, I have not defined any index file<br>
and I am calculating the g_velacc on backbone atoms.<br>
<br>
as the manual says, -aceflen will define the number of frames to be<br>
taken into consideration i suppose.<br>
<br>
Here, though with the option -s we are calculting the momentum auto<br>
correlation function, but still we are considering it as velocity<br>
auto correlation funciton. Is it alright or as the other user<br>
mentioned we need to devide the correlation value with square of the<br>
mass of the protein ?<br>
<br>
g_analyze:<br>
<br>
here, the numerical integration is done by trapezium rule. Ideally<br>
we need to carryout the integration from 0 to infinity but since our<br>
auto correlation function is calculated on a short period of time<br>
(which is close to t=0), the integration is evaluated only on this<br>
period i suppose. The output I got is the following:<br>
<br>
<br>
Calculating the integral using the trapezium rule<br>
Integral 1 0.99279 +/- 0.00000<br>
std. dev. relative deviation of<br>
standard --------- cumulants from<br>
those of<br>
set average deviation sqrt(n-1) a Gaussian<br>
distribition<br>
cum. 3 cum. 4<br>
SS1 3.975160e-02 1.960813e-01 4.002493e-02 2.939 6.669<br>
<br>
<br>
is the 0.99279 is the integral value or any thing else ? Which value<br>
I can compare with the value obtained by g_msd. My g_msd value is<br>
1.7*10^-6 cm**2/s which is reasonably good compared to the<br>
experimental value.<br>
<br>
<br>
Thanks and Regards,<br>
Ram.<br>
<br>
<br>
On Sun, Aug 31, 2008 at 2:18 PM, rams rams <<a href="mailto:rams.crux@gmail.com" target="_blank">rams.crux@gmail.com</a><br></div></div><div class="Ih2E3d">
<mailto:<a href="mailto:rams.crux@gmail.com" target="_blank">rams.crux@gmail.com</a>>> wrote:<br>
<br>
How to monitor the motion of center of mass of a protein as it<br>
is the case all the time to monitor this during the calculations<br>
of diffusion and correlation functions. How far the values will<br>
be different if we monitor the motion of backbone atoms rather<br>
than the center of mass motion.<br>
<br>
I still dont have any idea how to get the diffusion constant<br>
using g_velacc.<br>
<br>
Ram.<br>
<br>
On Sun, Aug 31, 2008 at 4:28 AM, Vitaly Chaban<br></div><div class="Ih2E3d">
<<a href="mailto:chaban@univer.kharkov.ua" target="_blank">chaban@univer.kharkov.ua</a> <mailto:<a href="mailto:chaban@univer.kharkov.ua" target="_blank">chaban@univer.kharkov.ua</a>>> wrote:<br>
<br>
> No special reason, just mundane ones: computing the<br>
diffusion constant<br>
> through mean square displacement is easier in terms of<br>
convergence.<br>
<br>
But it is not applicable in the anisotropic systems, for<br>
example in<br>
ones with spatial confinements present... :)<br>
<br>
<br>
<br>
--<br>
Vitaly V. Chaban<br>
School of Chemistry<br>
National University of Kharkiv<br>
Svoboda sq.,4, Kharkiv 61077, Ukraine<br>
email: <a href="mailto:chaban@univer.kharkov.ua" target="_blank">chaban@univer.kharkov.ua</a><br></div>
<mailto:<a href="mailto:chaban@univer.kharkov.ua" target="_blank">chaban@univer.kharkov.ua</a>><div class="Ih2E3d"><br>
skype: vvchaban<br>
<br>
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<br><div class="Ih2E3d">
<br>
-- <br>
David van der Spoel, Ph.D., Professor of Biology<br>
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.<br>
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org" target="_blank">spoel@gromacs.org</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br>
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