[gmx-users] Re: g_velacc

Florian Dommert dommert at fias.uni-frankfurt.de
Sun Aug 31 00:26:46 CEST 2008


  regard the topic about calculating diffusion coefficients, I also  
have a question regarding the code of g_velacc.
To calcalute the diffusion coefficient of a molecule with the help of  
its VACF, I think the center of mass velocity the protein is required.  
However there is no possibility to extract the VACF of molecule  
directly from a trajectory because g_velacc does not calulate VACFs of  
molecules, only Momentum ACFs. To finally obtain the VACF of molecule  
you have to divide the MACF of a molecule through the square of the  
mass of the molecule.

Is there a special reason, why it is not possible to get the VACF for  
a molecule straightforward from g_velacc ?

Best Regards


On 30.08.2008, at 18:02, rams rams wrote:

> Hi,
> Thanks to David van der Spoel and Vitaly Chaban for their valuable  
> suggestions regarding the calculation of diffusion constants.
> I did used the option -acflen with default values and focussed on  
> the region close to t=0. This time my plot looks fine though the  
> decay is not smooth (rather it is a sharp decay and then parallel to  
> time access). Now I would like to know how to get the diffusion  
> constant from this.
> It appears to me like I need to integrate this correlation funtion  
> to obtain the diffusion constant (does -integrate option in  
> g_analyze helpful ?) or any other way I can get this.
> I also found a reasonably good value this time (in comparison to  
> experiments for my diffusion constatns using g_msd). I want to make  
> a comparison between the values obtained by einstein and Green-kubo  
> relations.
> Thanks in advance.
> Ram.
> On Fri, Aug 29, 2008 at 5:32 PM, rams rams <rams.crux at gmail.com>  
> wrote:
> Dear Users,
> I am trying to calculate the velocity correlation functions to  
> estimate the diffusion constant of my protein which is having nearly  
> 50 residues. I am using the following command:
> g_velacc -f .trr -s .tpr -n .ndx -o .xvg -fitfn exp
> the output is the following:
> COR:
> COR: Correlation time (plain integral from  0.000 to 2500.000 ps) =   
> 0.90300 ps
> COR: Relaxation times are computed as fit to an exponential:
> COR:   y = exp(-x/a1)
> COR: Fit to correlation function from  0.000 ps to 2500.000 ps,  
> results in a
> COR:   Fit from   Integral Tail Value   Sum (ps)    a1 (ps)
> COR: 0.0000e+00 0.0000e+00 1.0458e-01 1.0458e-01  1.0458e-01
> I have no idea about the output to understand. I understood it is  
> trying to fit to the equation it displayed but have no idea about  
> the number 0.90300 ps.
> The .xvg plot I got is so surprising its just a straight line  
> parallel to time axis. I am sure I am making some mistake as I am  
> using g_velacc for the first time.
> From this if we want  to get the Diffusion coefficient we need to  
> integrate the correlation time from 0 to infinitive as it is  
> described in the manual. Is there any way we can do it by using any  
> of the options or we need to do it separately by using any other  
> tools ? If so please let me know.
> I also wanted to know the following things:
> What does the following options do:
> -normalize
> -integrate (in g_analyze)
> -fitfn (there are couple of options are given if any one have idea  
> about the sources for them ?)
> I calculated the diffusion coefficients using g_msd also, it gave  
> the diffusion coefficient value as 6.0*10^-6. Which is quite large  
> compared to the values reported in the literature which are around  
> 2.0*10^-6. Whats going wrong here also it is not generating the  
> output .xvg file. (It is complaining input/output fatal error).
> Thanks in advance,
> Ram.
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Florian Dommert

Computational and Theoretical Softmatter & Biophysics group

Frankfurt Institute for Advanced Studies
Johann-Wolfgang-Goethe University

Ruth-Moufang-Str. 1
60438 Frankfurt am Main

Phone: +49(0)69 / 798 - 47522
Fax:   +49(0)69 / 798 - 47611

EMail: dommert at fias.uni-frankfurt.de
Home: http://fias.uni-frankfurt.de/~simbio/Florian_Dommert

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