Dear users, I have a very basic question in MSD calculation. g_msd calculation on a protein dimer (~237 aa each) trajectory gave a plot of msd, with the values ranging between 1 to 14nm^2. But is this a sensible MSD? As the values given in a paper i was referring was in Ang^2 J. Chem. Theory Comput. 2012, 8, 1129-1142
Command that i used - echo 3 3 |g_msd -f a.xtc -s a.tpr -o a.xvg -n a.ndx -trestart 10 -b 4000 -e 50000 -rmcomm Is the range of diffusion coefficient of proteins of in water l in the range of x e-5 cm^2/s? (hemoglobin is 0.1 e-5 cm^2/s) Thank you kavya -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
