[gmx-users] Re: g_velacc

rams rams rams.crux at gmail.com
Mon Sep 1 17:54:11 CEST 2008

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  -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 ?


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,

On Sun, Aug 31, 2008 at 2:18 PM, rams rams <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>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
>> skype: vvchaban
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