Hi David Van der Spoel, You are right I missed the "dt" factor in the integral. Thanks a lot.
Ram. On Mon, Sep 1, 2008 at 2:52 PM, David van der Spoel <[EMAIL PROTECTED]>wrote: > 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 >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search >> before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [EMAIL PROTECTED] >> <mailto:[EMAIL PROTECTED]>. >> Can't post? Read >> http://www.gromacs.org/mailing_lists/users.php >> >> >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to [EMAIL PROTECTED] >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > -- > 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. > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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