rams rams wrote:
Hi Vitaly Chaban,
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 ?
yes. integration adds time in the denominator.
Ram.
On Mon, Sep 1, 2008 at 11:54 AM, rams rams <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> wrote:
Dear Vitaly Chaban,
Thanks for your kind sugestions. I did followed the way you
mentioned for calcualting the diffusion constants. I like to have a
better understanding of what I have done.
g_velacc:
g_velacc -f -s -o -aceflen
Since, mine is a single protein, I have not defined any index file
and I am calculating the g_velacc on backbone atoms.
as the manual says, -aceflen will define the number of frames to be
taken into consideration i suppose.
Here, though with the option -s we are calculting the momentum auto
correlation function, but still we are considering it as velocity
auto correlation funciton. Is it alright or as the other user
mentioned we need to devide the correlation value with square of the
mass of the protein ?
g_analyze:
here, the numerical integration is done by trapezium rule. Ideally
we need to carryout the integration from 0 to infinity but since our
auto correlation function is calculated on a short period of time
(which is close to t=0), the integration is evaluated only on this
period i suppose. The output I got is the following:
Calculating the integral using the trapezium rule
Integral 1 0.99279 +/- 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 3.975160e-02 1.960813e-01 4.002493e-02 2.939 6.669
is the 0.99279 is the integral value or any thing else ? Which value
I can compare with the value obtained by g_msd. My g_msd value is
1.7*10^-6 cm**2/s which is reasonably good compared to the
experimental value.
Thanks and Regards,
Ram.
On Sun, Aug 31, 2008 at 2:18 PM, rams rams <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> wrote:
How to monitor the motion of center of mass of a protein as it
is the case all the time to monitor this during the calculations
of diffusion and correlation functions. How far the values will
be different if we monitor the motion of backbone atoms rather
than the center of mass motion.
I still dont have any idea how to get the diffusion constant
using g_velacc.
Ram.
On Sun, Aug 31, 2008 at 4:28 AM, Vitaly Chaban
<[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>> wrote:
> No special reason, just mundane ones: computing the
diffusion constant
> through mean square displacement is easier in terms of
convergence.
But it is not applicable in the anisotropic systems, for
example in
ones with spatial confinements present... :)
--
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>
skype: vvchaban
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