Hi Everyone,<div><br></div><div>I have been trying to calculate diffusion coefficient for water. I am trying to reproduce the numbers published in journal papers.</div><div>I am using SPCE water model. I use the g_msd analysis tool.</div>
<div><br></div><div>g_msd -f traj.trr -n index.ndx -s npt.tpr -b 2 -e 8 </div><div><br></div><div>I use a box of volume 6x6x6 nm^3 which has 7161 water molecules. I equilibriate the system for a ns and then run for additional 10 ps for analysis. Here are some of the numbers that i get </div>
<div><br></div><div><span class="Apple-style-span" style="font-family: Cambria; font-size: 16px; ">a. With <span class="Apple-style-span" style="font-family: arial; font-size: small; ">Berendsen's T coupling and P coupling on i get <span class="Apple-style-span" style="font-family: Cambria; font-size: 16px; ">4.4941 (+/- 0.2992) 1e-5 cm^2/s</span></span></span></div>
<div>b. With Berendsen's T coupling on and P coupling off I get <span class="Apple-style-span" style="font-family: Cambria; font-size: 16px; ">3.2469 (+/- 0.1076) 1e-5 cm^2/s</span></div><div><span class="Apple-style-span" style="font-family: Cambria; font-size: 16px; ">c. <span class="Apple-style-span" style="font-family: arial; font-size: small; ">With Berendsen's T coupling on and P coupling off for 1ns and then T,P coupling both off (for analysis part) i get 2.8085 (+/- 0.0310) 1e-5 cm^2/s .</span></span></div>
<div><br></div><div>c is closest to the widely accepted experimental value of 2.3 1e-5 cm^2/s but its not quite right. </div><div><br></div><div>Could someone explain to me why the values obtained in above 3 cases are widely different and may be give some tips about the right procedure to calculate diffusion (method and invoking the g_msd tool)? </div>
<div><br></div><div>Thank you</div><div>Amit</div><div><br></div>