Dear Sir, Yes it is the same protein. Initially I had not superposed the structures in the trajectory. But this time I calculated the msd on a superposed trajectory (of the same simulation). the simulation is carried out on a dimer for 50ns using OPLS-AA and TIP4P water model. Using Gromacs4.5.3. If any other information is required Please let me know.
Thank you Kavya On Thu, Feb 7, 2013 at 5:28 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 2/7/13 6:49 AM, Kavyashree M wrote: > >> 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? >> >> > Are you studying the same protein? Given sparse detail in an email > thread, not knowing whether the simulations were done correctly or for > sufficient time, no one can assess correctness here. > > -Justin > > 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://vt.edu/Pages/Personal/justin> >>> <h**ttp://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> >>> <htt**p://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<h**ttp://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> >>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> > >>> >>> > -- > ==============================**========== > > 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
