[gmx-users] Re: g_velacc

[David van der Spoel]

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 <rams.crux at gmail.com 
> <mailto:rams.crux at gmail.com>> 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 <rams.crux at gmail.com
>     <mailto:rams.crux at gmail.com>> 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
>         <chaban at univer.kharkov.ua <mailto:chaban at univer.kharkov.ua>> 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: chaban at univer.kharkov.ua
>             <mailto:chaban at univer.kharkov.ua>
>             skype: vvchaban
> 
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> 
> 
> 
> 
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se