[gmx-users] Re: g_velacc
rams rams
rams.crux at gmail.com
Mon Sep 1 21:56:59 CEST 2008
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 <spoel at xray.bmc.uu.se>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 <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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>
>
> --
> 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
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