<div dir="ltr">Hi,<br><br>Thanks to David van der Spoel and Vitaly Chaban for their valuable suggestions regarding the calculation of diffusion constants.<br><br>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.<br>
<br>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.<br><br>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.<br>
<br>Thanks in advance.<br><br>Ram.<br><br><div class="gmail_quote">On Fri, Aug 29, 2008 at 5:32 PM, rams rams <span dir="ltr"><<a href="mailto:rams.crux@gmail.com">rams.crux@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div dir="ltr">Dear Users,<br><br>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:<br><br>g_velacc -f .trr -s .tpr -n .ndx -o .xvg -fitfn exp<br>
<br>the output is the following:<br><br>COR:<br>COR: Correlation time (plain integral from 0.000 to 2500.000 ps) = 0.90300 ps<br>COR: Relaxation times are computed as fit to an exponential:<br>COR: y = exp(-x/a1)<br>
COR: Fit to correlation function from 0.000 ps to 2500.000 ps, results in a<br>
COR: Fit from Integral Tail Value Sum (ps) a1 (ps) <br>COR: 0.0000e+00 0.0000e+00 1.0458e-01 1.0458e-01 1.0458e-01<br><br>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.<br>
<br>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.<br><br>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.<br>
<br>I also wanted to know the following things:<br><br>What does the following options do:<br><br>-normalize <br>-integrate (in g_analyze)<br><br>-fitfn (there are couple of options are given if any one have idea about the sources for them ?)<br>
<br>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).<br>
<br>Thanks in advance,<br>Ram.<br><br></div>
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