<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>