[gmx-users] Re: g_velacc

[rams rams]

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 <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> 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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>>
>>
>
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