Dear users, Since I am getting the mean square displacements in terms of several nm^2. I doubt it is wrong. Could anyone please explain me the solution for this. I checked the structure it is not denatured, In addition I used -rmcomm in order to remove the COM movements.
Kindly reply Thank you Kavya On Wed, Feb 6, 2013 at 3:35 PM, Kavyashree M <hmkv...@gmail.com> wrote: > 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 gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
