Dear Sir, Thank you for the reply,
It does not cross the boundary. I made the trajectory so that the dimers are together. I again calculated on a superposed trajectory, Then I got MSDs in the range of 0.01 to 0.15nm^2. But this is still higher than the value mentioned in the paper or is this acceptable? Thank you Kavya On Thu, Feb 7, 2013 at 4:54 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 2/6/13 11:49 PM, Kavyashree M wrote: > >> 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. >> >> > Sounds like a PBC issue. Does your dimer split across periodic > boundaries? If it does, then your MSD is going to go through the roof > because it's measuring the MSD of the whole protein. > > -Justin > > 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 >>> >>> >>> >>> > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- 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