<div dir="ltr">Dear users,<br><br>I am trying to calculate the diffusion coefficient for my protein using g_msd. I issued the following command:<br><br>g_msd -f .xtc -s .pdb -o .xvg<br><br>It
gave me the diffusion coefficient as 0.068 (+/- 0.0279) * 10^-5 cm^2 s^
-1 (for my whole system). The shape of the plot is not linear rather it is parabola (I think it might be due to the short period of simulation but I am not sure) <br><br>I also used g_analyze with the following commad:<br>
<br>g_analyze -f .xvg (the xvg from g_msd I have used here) -msd<br>
<br>This plot is linear but it considered only upto 5ns time period though my xtc/xvg file contains 10ns data. Could some one
tell me why g_analyze considered only 5ns simulation time. Also how
g_msd and g_analyze are different ?<br><br>I learnt form one of Xavier
Periole's postings, that g_msd is the instantaneous value of msd and
g_analyze is the average over the entire simulation. The diffusion
coefficient value I got <br>
is from g_msd, how can I calculate the value of the same by using g_analyze ? <br><br>Also, while calculating diffusion coefficient, is it better to monitor a particular atom or a group of atoms or entire protein ? <br><br>
Thanks and Regards.<br><br> </div>