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 ?
Ram. On Mon, Sep 1, 2008 at 11:54 AM, rams rams <[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]> 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]>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] >>> skype: vvchaban >>> >>> _______________________________________________ >>> 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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